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91 rows where devstage_curation = "Juvenile" and experiment.library_selection = "PolyA"

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tissue_curation 7

technology 2

experiment.library_layout 2

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 91 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Juvenile · 91 ✖
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
291 291 DRR224551 DRX214836 DRS236359 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf C SAMD00222582   sample name:42dpf C                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222582 DRX214836 42dpf C 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222582       14328721000.0 71643605.0 DRR224551 0:100 1:100 A:3545040254;C:3629416092;G:3695002549;T:3459108561;N:153544 100 100     3545040254 3629416092 3695002549 3459108561 153544 DRX214836 DRS236359 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.9671 0.95979 0.04174 0.04058 0.71867 0.72143 0.44818 0.46122 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
292 292 DRR224550 DRX214835 DRS236358 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf B SAMD00222581   sample name:42dpf B                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222581 DRX214835 42dpf B 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222581       14782437000.0 73912185.0 DRR224550 0:100 1:100 A:3652595601;C:3746189790;G:3788229051;T:3595263949;N:158609 100 100     3652595601 3746189790 3788229051 3595263949 158609 DRX214835 DRS236358 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96502 0.95776 0.0417 0.0399 0.71311 0.71423 0.46064 0.44469 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
293 293 DRR224549 DRX214834 DRS236357 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf A SAMD00222580   sample name:42dpf A                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222580 DRX214834 42dpf A 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222580       17895751600.0 89478758.0 DRR224549 0:100 1:100 A:4428562207;C:4525140210;G:4573827895;T:4368029340;N:191948 100 100     4428562207 4525140210 4573827895 4368029340 191948 DRX214834 DRS236357 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96506 0.96043 0.04654 0.0446 0.70956 0.71153 0.49143 0.48957 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
29188 29188 SRR8176753 SRX4996870 SRS4031878 SRP480945 PRJNA1055160 Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain PRJNA1055160 Other We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf   pubmed:38529407   Nadia 30dpf ZZ Gonad Single Cell RNA Seq Nadia 30dpf ZZ Gonad Single Cell RNA Seq   strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal                 scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad Nadia 30dpf ZZ gonad Nadia 30dpf ZZ gonad A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP480945   loader:fastq load.py     23587173438.0 167284918.0 1 I1 001.fastq.gz 0:8 1:133 A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374 8 133     6732844252 4934497997 5685086026 6219863789 14881374 SRX4996870 SRS4031878 SRA807619 University of Oregon|Institute of Neuroscience University of Oregon                       T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2018-11-08 Juvenile Juvenile Gonad Reproductive System
29189 29189 SRR8176754 SRX4996869 SRS4031877 SRP480945 PRJNA1055160 Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain PRJNA1055160 Other We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf   pubmed:38529407   Nadia 30dpf ZW Gonad Single Cell RNA Seq Nadia 30dpf ZW Gonad Single Cell RNA Seq   strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal                 scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad Nadia 30dpf ZW gonad Nadia 30dpf ZW gonad A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP480945   loader:fastq load.py     43358808480.0 307509280.0 2 I1 001.fastq.gz 0:8 1:133 A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487 8 133     12290612367 8880655083 10261318751 11898771792 27450487 SRX4996869 SRS4031877 SRA807619 University of Oregon|Institute of Neuroscience University of Oregon                       T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2018-11-08 Juvenile Juvenile Gonad Reproductive System
31932 31932 SRR28776262 SRX24341224 SRS21101374 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 3 Ablated rep3   strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 105 P2276 105 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_105_1.fastq.gz 5_150903_BC7FRTANXX_P2276_105_2.fastq.gz fastq fastq 12443422824.0 49378662.0 5 150903 BC7FRTANXX P2276 105 1.fastq.gz 0:126 1:126 A:3354062616;C:2842732118;G:2899611331;T:3337717349;N:9299410 126 126     3354062616 2842732118 2899611331 3337717349 9299410 SRX24341224 SRS21101374 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31933 31933 SRR28776263 SRX24341223 SRS21101373 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 2 Ablated rep2   strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 103 P2276 103 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_103_1.fastq.gz 5_150903_BC7FRTANXX_P2276_103_2.fastq.gz fastq fastq 12508569612.0 49637181.0 5 150903 BC7FRTANXX P2276 103 1.fastq.gz 0:126 1:126 A:3285561592;C:2941406523;G:2987518362;T:3285515692;N:8567443 126 126     3285561592 2941406523 2987518362 3285515692 8567443 SRX24341223 SRS21101373 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31934 31934 SRR28776264 SRX24341222 SRS21101372 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 1 Ablated rep1   strain:AB|age:2 mpf date:2015 06 04|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 101 P2276 101 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_101_1.fastq.gz 5_150903_BC7FRTANXX_P2276_101_2.fastq.gz fastq fastq 12536188812.0 49746781.0 5 150903 BC7FRTANXX P2276 101 1.fastq.gz 0:126 1:126 A:3281688237;C:2958476935;G:3022979051;T:3265495888;N:7548701 126 126     3281688237 2958476935 3022979051 3265495888 7548701 SRX24341222 SRS21101372 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31935 31935 SRR28776265 SRX24341221 SRS21101375 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Control 2 Control rep2   strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 106 P2276 106 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_106_1.fastq.gz 5_150903_BC7FRTANXX_P2276_106_2.fastq.gz fastq fastq 11797087680.0 46813840.0 5 150903 BC7FRTANXX P2276 106 1.fastq.gz 0:126 1:126 A:3087253274;C:2787897503;G:2841312816;T:3072716302;N:7907785 126 126     3087253274 2787897503 2841312816 3072716302 7907785 SRX24341221 SRS21101375 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31936 31936 SRR28776266 SRX24341220 SRS21101371 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Control 1 Control rep1   strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 104 P2276 104 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_104_1.fastq.gz 5_150903_BC7FRTANXX_P2276_104_2.fastq.gz fastq fastq 13294186416.0 52754708.0 5 150903 BC7FRTANXX P2276 104 1.fastq.gz 0:126 1:126 A:3544892164;C:3073022881;G:3106419492;T:3559768207;N:10083672 126 126     3544892164 3073022881 3106419492 3559768207 10083672 SRX24341220 SRS21101371 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
34397 34397 SRR31719829 SRX27082407 SRS23541575 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression normal diet for 35 days RNAseq MASLD HepGOE ND rep2 HepGOE ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 10|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of normal diet. HepGOE ND rep2 HepGOE ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_ND_rep2_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep2_2.fq.gz fastq fastq 7177536600.0 23925122.0 RNAseq MASLD HepGOE ND rep2 1.fq.gz 0:150 1:150 A:1917334205;C:1668595888;G:1703080664;T:1887679182;N:846661 150 150     1917334205 1668595888 1703080664 1887679182 846661 SRX27082407 SRS23541575 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34398 34398 SRR31719830 SRX27082406 SRS23541574 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression normal diet for 35 days RNAseq MASLD HepGOE ND rep1 HepGOE ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of normal diet. HepGOE ND rep1 HepGOE ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_ND_rep1_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep1_2.fq.gz fastq fastq 6621268500.0 22070895.0 RNAseq MASLD HepGOE ND rep1 1.fq.gz 0:150 1:150 A:1711419517;C:1595902037;G:1611514825;T:1702282385;N:149736 150 150     1711419517 1595902037 1611514825 1702282385 149736 SRX27082406 SRS23541574 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34399 34399 SRR31719831 SRX27082405 SRS23541573 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days RNAseq MASLD HepGKO HFC rep2 HepGKO HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet. HepGKO HFC rep2 HepGKO HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep2_2.fq.gz fastq fastq 5901646500.0 19672155.0 RNAseq MASLD HepGKO HFC rep2 1.fq.gz 0:150 1:150 A:1547939419;C:1401111812;G:1425197669;T:1527300198;N:97402 150 150     1547939419 1401111812 1425197669 1527300198 97402 SRX27082405 SRS23541573 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34400 34400 SRR31719832 SRX27082404 SRS23541572 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days RNAseq MASLD HepGKO HFC rep1 HepGKO HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet. HepGKO HFC rep1 HepGKO HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep1_2.fq.gz fastq fastq 6484178700.0 21613929.0 RNAseq MASLD HepGKO HFC rep1 1.fq.gz 0:150 1:150 A:1692850957;C:1545705390;G:1573644279;T:1671871368;N:106706 150 150     1692850957 1545705390 1573644279 1671871368 106706 SRX27082404 SRS23541572 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34401 34401 SRR31719833 SRX27082403 SRS23541571 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout normal diet for 35 days RNAseq MASLD HepGKO ND rep2 HepGKO ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of normal diet. HepGKO ND rep2 HepGKO ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_ND_rep2_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep2_2.fq.gz fastq fastq 6436941000.0 21456470.0 RNAseq MASLD HepGKO ND rep2 1.fq.gz 0:150 1:150 A:1671402056;C:1543860294;G:1570976721;T:1650596456;N:105473 150 150     1671402056 1543860294 1570976721 1650596456 105473 SRX27082403 SRS23541571 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34402 34402 SRR31719834 SRX27082402 SRS23541570 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout normal diet for 35 days RNAseq MASLD HepGKO ND rep1 HepGKO ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of normal diet. HepGKO ND rep1 HepGKO ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_ND_rep1_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep1_2.fq.gz fastq fastq 6386174700.0 21287249.0 RNAseq MASLD HepGKO ND rep1 1.fq.gz 0:150 1:150 A:1662767742;C:1527603435;G:1545756971;T:1649944714;N:101838 150 150     1662767742 1527603435 1545756971 1649944714 101838 SRX27082402 SRS23541570 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34403 34403 SRR31719835 SRX27082401 SRS23541569 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish high fat high cholesterol diet for 35 days RNAseq MASLD WT HFC rep2 WT HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet. WT HFC rep2 WT HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_HFC_rep2_1.fq.gz RNAseq_MASLD_WT_HFC_rep2_2.fq.gz fastq fastq 7088163900.0 23627213.0 RNAseq MASLD WT HFC rep2 1.fq.gz 0:150 1:150 A:1904609517;C:1635475353;G:1664944747;T:1882978732;N:155551 150 150     1904609517 1635475353 1664944747 1882978732 155551 SRX27082401 SRS23541569 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34404 34404 SRR31719836 SRX27082400 SRS23541568 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish high fat high cholesterol diet for 35 days RNAseq MASLD WT HFC rep1 WT HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet. WT HFC rep1 WT HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_HFC_rep1_1.fq.gz RNAseq_MASLD_WT_HFC_rep1_2.fq.gz fastq fastq 7053396600.0 23511322.0 RNAseq MASLD WT HFC rep1 1.fq.gz 0:150 1:150 A:1862942395;C:1655266768;G:1688002812;T:1847030526;N:154099 150 150     1862942395 1655266768 1688002812 1847030526 154099 SRX27082400 SRS23541568 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34405 34405 SRR31719837 SRX27082399 SRS23541567 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days RNAseq MASLD HepGOE HFC rep2 HepGOE HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 12|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet. HepGOE HFC rep2 HepGOE HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep2_2.fq.gz fastq fastq 7004757600.0 23349192.0 RNAseq MASLD HepGOE HFC rep2 1.fq.gz 0:150 1:150 A:1846708800;C:1647727254;G:1676955416;T:1833207397;N:158733 150 150     1846708800 1647727254 1676955416 1833207397 158733 SRX27082399 SRS23541567 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34406 34406 SRR31719838 SRX27082398 SRS23541566 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days RNAseq MASLD HepGOE HFC rep1 HepGOE HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 11|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet. HepGOE HFC rep1 HepGOE HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep1_2.fq.gz fastq fastq 8211524400.0 27371748.0 RNAseq MASLD HepGOE HFC rep1 1.fq.gz 0:150 1:150 A:2217820195;C:1876471113;G:1906298333;T:2210753213;N:181546 150 150     2217820195 1876471113 1906298333 2210753213 181546 SRX27082398 SRS23541566 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34407 34407 SRR31719839 SRX27082397 SRS23541565 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish normal diet for 35 days RNAseq MASLD WT ND rep2 WT ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of normal diet. WT ND rep2 WT ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_ND_rep2_1.fq.gz RNAseq_MASLD_WT_ND_rep2_2.fq.gz fastq fastq 6966786300.0 23222621.0 RNAseq MASLD WT ND rep2 1.fq.gz 0:150 1:150 A:1855652140;C:1619780884;G:1651213951;T:1839982276;N:157049 150 150     1855652140 1619780884 1651213951 1839982276 157049 SRX27082397 SRS23541565 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34408 34408 SRR31719840 SRX27082396 SRS23541564 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish normal diet for 35 days RNAseq MASLD WT ND rep1 WT ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of normal diet. WT ND rep1 WT ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_ND_rep1_1.fq.gz RNAseq_MASLD_WT_ND_rep1_2.fq.gz fastq fastq 7149668700.0 23832229.0 RNAseq MASLD WT ND rep1 1.fq.gz 0:150 1:150 A:1869145140;C:1695095352;G:1726444600;T:1858824841;N:158767 150 150     1869145140 1695095352 1726444600 1858824841 158767 SRX27082396 SRS23541564 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
42350 42350 SRR7410374 SRX4281985 SRS3446891 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl wildtype 30dpf fancl wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 29 30dpf fancl wild type 30 29 30dpf fancl wild type 30 29 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         2995334748.0 11886249.0 fancl wt 30 29 R1.fq.gz 0:126 1:126 A:744191069;C:728333183;G:750401765;T:772070330;N:338401 126 126     744191069 728333183 750401765 772070330 338401 SRX4281985 SRS3446891 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.94282 0.94989 0.10261 0.10127 0.72119 0.72498 0.56397 0.58255 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42353 42353 SRR7410377 SRX4281982 SRS3446891 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl wildtype 30dpf fancl wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 23 30dpf fancl wild type 30 23 30dpf fancl wild type 30 23 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         4941076140.0 19607445.0 fancl wt 30 23 R1.fq.gz 0:126 1:126 A:1238002112;C:1200211717;G:1228052007;T:1274235738;N:574566 126 126     1238002112 1200211717 1228052007 1274235738 574566 SRX4281982 SRS3446891 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.94867 0.95506 0.10325 0.10339 0.72683 0.72961 0.58661 0.58503 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42376 42376 SRR7410400 SRX4281959 SRS3446891 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl wildtype 30dpf fancl wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 02 30dpf fancl wild type 30 02 30dpf fancl wild type 30 02 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         5095936944.0 20221972.0 fancl wt 30 02 R1.fq.gz 0:126 1:126 A:1263289375;C:1249199634;G:1278613652;T:1304252815;N:581468 126 126     1263289375 1249199634 1278613652 1304252815 581468 SRX4281959 SRS3446891 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.94816 0.95396 0.10228 0.10104 0.72616 0.72654 0.57393 0.58353 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42396 42396 SRR7410420 SRX4281939 SRS3446903 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl mutant 30dpf fancl mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 17 30dpf fancl mutant 30 17 30dpf fancl mutant 30 17 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         7715826468.0 30618359.0 fancl mut 30 17 R2.fq.gz 0:126 1:126 A:1807986336;C:2002774910;G:2035877968;T:1868285117;N:902137 126 126     1807986336 2002774910 2035877968 1868285117 902137 SRX4281939 SRS3446903 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.96709 0.97354 0.08768 0.08676 0.74152 0.7447 0.58802 0.57631 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42397 42397 SRR7410421 SRX4281938 SRS3446903 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl mutant 30dpf fancl mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 08 30dpf fancl mutant 30 08 30dpf fancl mutant 30 08 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         5683582044.0 22553897.0 fancl mut 30 08 R1.fq.gz 0:126 1:126 A:1407291490;C:1395013891;G:1423770166;T:1456844244;N:662253 126 126     1407291490 1395013891 1423770166 1456844244 662253 SRX4281938 SRS3446903 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.9455 0.95135 0.1075 0.10757 0.71912 0.72196 0.57287 0.55078 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42398 42398 SRR7410422 SRX4281937 SRS3446903 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl mutant 30dpf fancl mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 01 30dpf fancl mutant 30 01 30dpf fancl mutant 30 01 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         8917768188.0 35387969.0 fancl mut 30 01 R1.fq.gz 0:126 1:126 A:2184330162;C:2213012086;G:2262881514;T:2256511021;N:1033405 126 126     2184330162 2213012086 2262881514 2256511021 1033405 SRX4281937 SRS3446903 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.95002 0.95663 0.11136 0.11179 0.72502 0.72815 0.57109 0.54445 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42404 42404 SRR7410428 SRX4281931 SRS3446903 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl mutant 30dpf fancl mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 25 30dpf fancl mutant 30 25 30dpf fancl mutant 30 25 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         10430314776.0 41390138.0 fancl mut 30 25 R1.fq.gz 0:126 1:126 A:2601755089;C:2535322569;G:2600718638;T:2691288565;N:1229915 126 126     2601755089 2535322569 2600718638 2691288565 1229915 SRX4281931 SRS3446903 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.94533 0.95212 0.10271 0.10301 0.71549 0.71823 0.57327 0.58016 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42405 42405 SRR7410429 SRX4281930 SRS3446903 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl mutant 30dpf fancl mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 19 30dpf fancl mutant 30 19 30dpf fancl mutant 30 19 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         5726761488.0 22725244.0 fancl mut 30 19 R2.fq.gz 0:126 1:126 A:1417828651;C:1399791137;G:1432389082;T:1476078215;N:674403 126 126     1417828651 1399791137 1432389082 1476078215 674403 SRX4281930 SRS3446903 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.94187 0.95012 0.10759 0.10798 0.71944 0.71928 0.57165 0.52896 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42416 42416 SRR7410440 SRX4281919 SRS3446900 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 wildtype 30dpf brca2 wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 27 30dpf brca2 wild type 30 27 30dpf brca2 wild type 30 27 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         10335588808.0 34223804.0 brca2 wt 30 27 TATGTGGC R2.fq.gz 0:151 1:151 A:2578068515;C:2550705556;G:2592943796;T:2612664094;N:1206847 151 151     2578068515 2550705556 2592943796 2612664094 1206847 SRX4281919 SRS3446900 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91509 0.92944 0.1198 0.09246 0.72794 0.73476 0.50295 0.55616 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42417 42417 SRR7410441 SRX4281918 SRS3446900 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 wildtype 30dpf brca2 wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 19 30dpf brca2 wild type 30 19 30dpf brca2 wild type 30 19 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         16971362932.0 56196566.0 brca2 wt 30 19 TTCAGCTC R1.fq.gz 0:151 1:151 A:4261370563;C:4149954129;G:4237743108;T:4320302899;N:1992233 151 151     4261370563 4149954129 4237743108 4320302899 1992233 SRX4281918 SRS3446900 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90172 0.92611 0.10946 0.08762 0.71551 0.71993 0.50428 0.59503 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42418 42418 SRR7410442 SRX4281917 SRS3446900 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 wildtype 30dpf brca2 wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 14 30dpf brca2 wild type 30 14 30dpf brca2 wild type 30 14 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         6864849882.0 22731291.0 brca2 wt 30 14 TTGCGTAC R2.fq.gz 0:151 1:151 A:1727616237;C:1676798537;G:1712647063;T:1746990291;N:797754 151 151     1727616237 1676798537 1712647063 1746990291 797754 SRX4281917 SRS3446900 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.92049 0.93514 0.11 0.08759 0.73511 0.74349 0.51728 0.58993 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42420 42420 SRR7410444 SRX4281915 SRS3446900 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 wildtype 30dpf brca2 wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 17 30dpf brca2 wild type 30 17 30dpf brca2 wild type 30 17 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         8432584732.0 27922466.0 brca2 wt 30 17 TGCGTGAA R2.fq.gz 0:151 1:151 A:2132479978;C:2035633473;G:2088942653;T:2174550395;N:978233 151 151     2132479978 2035633473 2088942653 2174550395 978233 SRX4281915 SRS3446900 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91011 0.9287 0.1076 0.08793 0.70627 0.71431 0.49536 0.58516 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42421 42421 SRR7410445 SRX4281914 SRS3446900 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 wildtype 30dpf brca2 wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 16 30dpf brca2 wild type 30 16 30dpf brca2 wild type 30 16 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         5787544912.0 19164056.0 brca2 wt 30 16 TTGACTCT R1.fq.gz 0:151 1:151 A:1470953427;C:1394911620;G:1427129077;T:1493879392;N:671396 151 151     1470953427 1394911620 1427129077 1493879392 671396 SRX4281914 SRS3446900 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90129 0.91879 0.11795 0.09608 0.69909 0.70818 0.49724 0.5781 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42441 42441 SRR7410465 SRX4281894 SRS3446892 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 mutant 30dpf brca2 mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 13 30dpf brca2 mutant 30 13 30dpf brca2 mutant 30 13 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         7614746082.0 25214391.0 brca2 mut 30 13 GTGTCCTT R2.fq.gz 0:151 1:151 A:1953796672;C:1825224132;G:1858553376;T:1976291422;N:880480 151 151     1953796672 1825224132 1858553376 1976291422 880480 SRX4281894 SRS3446892 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90472 0.92046 0.1248 0.1051 0.69836 0.70745 0.43736 0.58121 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42442 42442 SRR7410466 SRX4281893 SRS3446892 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 mutant 30dpf brca2 mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 12 30dpf brca2 mutant 30 12 30dpf brca2 mutant 30 12 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         6609294160.0 21885080.0 brca2 mut 30 12 TGTTCTCC R1.fq.gz 0:151 1:151 A:1663996252;C:1611724064;G:1649391730;T:1683416159;N:765955 151 151     1663996252 1611724064 1649391730 1683416159 765955 SRX4281893 SRS3446892 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.92261 0.93707 0.12282 0.10062 0.72555 0.73655 0.50213 0.55978 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42443 42443 SRR7410467 SRX4281892 SRS3446892 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 mutant 30dpf brca2 mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 11 30dpf brca2 mutant 30 11 30dpf brca2 mutant 30 11 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         3609770062.0 11952881.0 brca2 mut 30 11 ATCACGTT R2.fq.gz 0:151 1:151 A:910534494;C:877404076;G:898143524;T:923267603;N:420365 151 151     910534494 877404076 898143524 923267603 420365 SRX4281892 SRS3446892 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90353 0.92062 0.11856 0.09432 0.72809 0.73669 0.44186 0.57479 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42447 42447 SRR7410471 SRX4281888 SRS3446892 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 mutant 30dpf brca2 mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 36 30dpf brca2 mutant 30 36 30dpf brca2 mutant 30 36 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         6899944698.0 22847499.0 brca2 mut 30 36 GAGGTGCT R1.fq.gz 0:151 1:151 A:1745582542;C:1669300984;G:1707455172;T:1776814198;N:791802 151 151     1745582542 1669300984 1707455172 1776814198 791802 SRX4281888 SRS3446892 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91438 0.93255 0.11037 0.09276 0.72088 0.73024 0.50255 0.57014 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42448 42448 SRR7410472 SRX4281887 SRS3446892 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library brca2 mutant 30dpf brca2 mutant 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:brca2 ZM 00057434 / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 18 30dpf brca2 mutant 30 18 30dpf brca2 mutant 30 18 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP151068         9162516316.0 30339458.0 brca2 mut 30 18 GTAAGGTG R2.fq.gz 0:151 1:151 A:2312465867;C:2223181568;G:2268715689;T:2357087788;N:1065404 151 151     2312465867 2223181568 2268715689 2357087788 1065404 SRX4281887 SRS3446892 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91218 0.93164 0.10691 0.08773 0.73464 0.74306 0.50561 0.58578 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
42450 42450 SRR7410474 SRX4281885 SRS3446891 SRP151068 PRJNA387484 RNA Seq of a Zebrafish Fanconi Mutant PRJNA387484 Transcriptome Analysis We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.     RNA seq library fancl wildtype 30dpf fancl wildtype 30dpf   strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait University of Oregon|genotype:fancl nkhg10aEt +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 30 30dpf fancl wild type 30 30 30dpf fancl wild type 30 30 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP151068         10131111648.0 40202824.0 fancl wt 30 30 R1.fq.gz 0:126 1:126 A:2542923952;C:2446585748;G:2508652587;T:2631768070;N:1181291 126 126     2542923952 2446585748 2508652587 2631768070 1181291 SRX4281885 SRS3446891 SRA726408 University of Oregon|Institute of Neuroscience University of Oregon 2 0.94391 0.95296 0.107 0.10797 0.72786 0.73115 0.58931 0.57476 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-21 Juvenile Juvenile Whole Organism All anatomical structures
53654 53654 SRR10010335 SRX6748603 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 11 35dpf nr5a1a nr5a1b double mutant 11 35dpf nr5a1a nr5a1b double mutant 11 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-11_combined_R1.fq.gz nr5a1ab35dmut-11_combined_R2.fq.gz fastq fastq 5464020164.0 18092782.0 nr5a1ab35dmut 11 combined R1.fq.gz 0:151 1:151 A:1417197935;C:1238763491;G:1264099371;T:1543026312;N:933055 151 151     1417197935 1238763491 1264099371 1543026312 933055 SRX6748603 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.82573 0.85627 0.0768 0.06148 0.75704 0.76017 0.49566 0.58424 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53655 53655 SRR10010336 SRX6748602 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 7 35dpf nr5a1b mutant 7 35dpf nr5a1b mutant 7 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-7_combined_R1.fq.gz nr5a1b35dmut-7_combined_R2.fq.gz fastq fastq 2116406940.0 7007970.0 nr5a1b35dmut 7 combined R1.fq.gz 0:151 1:151 A:534677619;C:494553805;G:503529167;T:583343323;N:303026 151 151     534677619 494553805 503529167 583343323 303026 SRX6748602 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.89953 0.9204 0.08475 0.06359 0.75069 0.75615 0.5203 0.5919 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53656 53656 SRR10010337 SRX6748601 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 10 35dpf nr5a1a nr5a1b double mutant 10 35dpf nr5a1a nr5a1b double mutant 10 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-10_combined_R1.fq.gz nr5a1ab35dmut-10_combined_R2.fq.gz fastq fastq 3016366034.0 9987967.0 nr5a1ab35dmut 10 combined R1.fq.gz 0:151 1:151 A:752733986;C:720025699;G:731849549;T:811247600;N:509200 151 151     752733986 720025699 731849549 811247600 509200 SRX6748601 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90615 0.91707 0.11046 0.07981 0.74651 0.74966 0.49676 0.60165 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53657 53657 SRR10010338 SRX6748600 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 9 35dpf nr5a1a nr5a1b double mutant 9 35dpf nr5a1a nr5a1b double mutant 9 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-9_combined_R1.fq.gz nr5a1ab35dmut-9_combined_R2.fq.gz fastq fastq 3569050194.0 11818047.0 nr5a1ab35dmut 9 combined R1.fq.gz 0:151 1:151 A:899915774;C:849832234;G:859458329;T:959242263;N:601594 151 151     899915774 849832234 859458329 959242263 601594 SRX6748600 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.88978 0.9004 0.09772 0.07218 0.74799 0.74968 0.51174 0.6088 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53658 53658 SRR10010339 SRX6748599 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 2 35dpf nr5a1a nr5a1b double mutant 2 35dpf nr5a1a nr5a1b double mutant 2 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-2_combined_R1.fq.gz nr5a1ab35dmut-2_combined_R2.fq.gz fastq fastq 2828323922.0 9365311.0 nr5a1ab35dmut 2 combined R1.fq.gz 0:151 1:151 A:691090279;C:673032167;G:684529355;T:779155559;N:516562 151 151     691090279 673032167 684529355 779155559 516562 SRX6748599 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.8834 0.9068 0.11546 0.07455 0.75503 0.75615 0.51068 0.61929 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53659 53659 SRR10010340 SRX6748598 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 1 35dpf nr5a1a nr5a1b double mutant 1 35dpf nr5a1a nr5a1b double mutant 1 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-1_combined_R1.fq.gz nr5a1ab35dmut-1_combined_R2.fq.gz fastq fastq 3461567790.0 11462145.0 nr5a1ab35dmut 1 combined R1.fq.gz 0:151 1:151 A:863912807;C:826288038;G:844009627;T:926819831;N:537487 151 151     863912807 826288038 844009627 926819831 537487 SRX6748598 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90732 0.91778 0.10103 0.06771 0.74026 0.74619 0.50631 0.59632 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53660 53660 SRR10010341 SRX6748597 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 4 35dpf nr5a1b mutant 4 35dpf nr5a1b mutant 4 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-4_combined_R1.fq.gz nr5a1b35dmut-4_combined_R2.fq.gz fastq fastq 2823289582.0 9348641.0 nr5a1b35dmut 4 combined R1.fq.gz 0:151 1:151 A:692918043;C:667773087;G:683991041;T:778117057;N:490354 151 151     692918043 667773087 683991041 778117057 490354 SRX6748597 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.89649 0.92027 0.09415 0.06385 0.75463 0.75883 0.48098 0.58128 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53661 53661 SRR10010342 SRX6748596 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 14 35dpf nr5a1a nr5a1b double mutant 14 35dpf nr5a1a nr5a1b double mutant 14 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-14_combined_R1.fq.gz nr5a1ab35dmut-14_combined_R2.fq.gz fastq fastq 2662720410.0 8816955.0 nr5a1ab35dmut 14 combined R1.fq.gz 0:151 1:151 A:665577500;C:635869780;G:647241076;T:713592928;N:439126 151 151     665577500 635869780 647241076 713592928 439126 SRX6748596 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90062 0.91305 0.1132 0.08326 0.75339 0.7555 0.49702 0.59781 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53664 53664 SRR10010345 SRX6748593 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 1 35dpf nr5a1b mutant 1 35dpf nr5a1b mutant 1 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-1_combined_R1.fq.gz nr5a1b35dmut-1_combined_R2.fq.gz fastq fastq 3080371310.0 10199905.0 nr5a1b35dmut 1 combined R1.fq.gz 0:151 1:151 A:749979603;C:751889973;G:770422909;T:807597821;N:481004 151 151     749979603 751889973 770422909 807597821 481004 SRX6748593 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91959 0.93095 0.11586 0.07628 0.76187 0.76562 0.49454 0.57785 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53665 53665 SRR10010346 SRX6748592 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 2 35dpf nr5a1b mutant 2 35dpf nr5a1b mutant 2 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-2_combined_R1.fq.gz nr5a1b35dmut-2_combined_R2.fq.gz fastq fastq 3633938820.0 12032910.0 nr5a1b35dmut 2 combined R1.fq.gz 0:151 1:151 A:905316417;C:865468187;G:876812140;T:985720508;N:621568 151 151     905316417 865468187 876812140 985720508 621568 SRX6748592 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.8972 0.91027 0.11437 0.07781 0.74099 0.74446 0.4981 0.60461 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53676 53676 SRR10010357 SRX6748581 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 7 35dpf nr5a1a mutant 7 35dpf nr5a1a mutant 7 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-7_combined_R1.fq.gz nr5a1a35dmut-7_combined_R2.fq.gz fastq fastq 2969897294.0 9834097.0 nr5a1a35dmut 7 combined R1.fq.gz 0:151 1:151 A:752593200;C:695994377;G:707935979;T:812884925;N:488813 151 151     752593200 695994377 707935979 812884925 488813 SRX6748581 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.89218 0.906 0.09342 0.07022 0.73795 0.73898 0.51281 0.5911 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53677 53677 SRR10010358 SRX6748580 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 8 35dpf nr5a1a mutant 8 35dpf nr5a1a mutant 8 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-8_combined_R1.fq.gz nr5a1a35dmut-8_combined_R2.fq.gz fastq fastq 6225038118.0 20612709.0 nr5a1a35dmut 8 combined R1.fq.gz 0:151 1:151 A:1559098665;C:1505493891;G:1534176065;T:1625255981;N:1013516 151 151     1559098665 1505493891 1534176065 1625255981 1013516 SRX6748580 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90023 0.90282 0.09369 0.06592 0.73525 0.73854 0.50906 0.59368 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53678 53678 SRR10010359 SRX6748579 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 2 35dpf wild type 2 35dpf wild type 2 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-2_combined_R1.fq.gz nr5a1_35day_WT-2_combined_R2.fq.gz fastq fastq 4142275186.0 13716143.0 nr5a1 35day WT 2 combined R1.fq.gz 0:151 1:151 A:1055251193;C:967398418;G:984879234;T:1134062187;N:684154 151 151     1055251193 967398418 984879234 1134062187 684154 SRX6748579 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.89791 0.91014 0.09157 0.06806 0.73927 0.74067 0.515 0.58656 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53679 53679 SRR10010360 SRX6748578 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 3 35dpf wild type 3 35dpf wild type 3 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-3_combined_R2.fq.gz nr5a1_35day_WT-3_combined_R1.fq.gz fastq fastq 2471376532.0 8183366.0 nr5a1 35day WT 3 combined R1.fq.gz 0:151 1:151 A:615088670;C:576161730;G:582945558;T:696743565;N:437009 151 151     615088670 576161730 582945558 696743565 437009 SRX6748578 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.87753 0.90284 0.1111 0.07857 0.72563 0.72794 0.50927 0.59766 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53680 53680 SRR10010361 SRX6748577 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 4 35dpf wild type 4 35dpf wild type 4 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-4_combined_R1.fq.gz nr5a1_35day_WT-4_combined_R2.fq.gz fastq fastq 2116363754.0 7007827.0 nr5a1 35day WT 4 combined R1.fq.gz 0:151 1:151 A:517886726;C:489788898;G:502421580;T:605882187;N:384363 151 151     517886726 489788898 502421580 605882187 384363 SRX6748577 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.87446 0.91282 0.08961 0.06167 0.75325 0.75363 0.50444 0.58991 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53681 53681 SRR10010362 SRX6748576 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 5 35dpf wild type 5 35dpf wild type 5 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-5_combined_R1.fq.gz nr5a1_35day_WT-5_combined_R2.fq.gz fastq fastq 2730512464.0 9041432.0 nr5a1 35day WT 5 combined R1.fq.gz 0:151 1:151 A:676487187;C:641297195;G:648646413;T:763575356;N:506313 151 151     676487187 641297195 648646413 763575356 506313 SRX6748576 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.87293 0.89776 0.08726 0.06177 0.7727 0.77402 0.47624 0.58994 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53682 53682 SRR10010363 SRX6748575 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 6 35dpf wild type 6 35dpf wild type 6 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-6_combined_R1.fq.gz nr5a1_35day_WT-6_combined_R2.fq.gz fastq fastq 2539526758.0 8409029.0 nr5a1 35day WT 6 combined R1.fq.gz 0:151 1:151 A:654061696;C:592950317;G:606528343;T:685572585;N:413817 151 151     654061696 592950317 606528343 685572585 413817 SRX6748575 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.88978 0.89645 0.09493 0.07075 0.73509 0.73965 0.53187 0.55068 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53683 53683 SRR10010364 SRX6748574 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 9 35dpf wild type 9 35dpf wild type 9 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-9_combined_R1.fq.gz nr5a1_35day_WT-9_combined_R2.fq.gz fastq fastq 2585156844.0 8560122.0 nr5a1 35day WT 9 combined R1.fq.gz 0:151 1:151 A:659256640;C:603793032;G:616048994;T:705643382;N:414796 151 151     659256640 603793032 616048994 705643382 414796 SRX6748574 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90219 0.91318 0.11237 0.08413 0.74472 0.74799 0.52565 0.61427 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53688 53688 SRR10010369 SRX6748569 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 8 35dpf nr5a1b mutant 8 35dpf nr5a1b mutant 8 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-8_combined_R1.fq.gz nr5a1b35dmut-8_combined_R2.fq.gz fastq fastq 3225498920.0 10680460.0 nr5a1b35dmut 8 combined R1.fq.gz 0:151 1:151 A:810589172;C:772659409;G:785398777;T:856326001;N:525561 151 151     810589172 772659409 785398777 856326001 525561 SRX6748569 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.9048 0.9133 0.0825 0.05993 0.74627 0.74933 0.52212 0.58896 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53698 53698 SRR10010379 SRX6748559 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 10 35dpf wild type 10 35dpf wild type 10 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-10_combined_R1.fq.gz nr5a1_35day_WT-10_combined_R2.fq.gz fastq fastq 3038724000.0 10062000.0 nr5a1 35day WT 10 combined R1.fq.gz 0:151 1:151 A:764571339;C:715912069;G:728730982;T:828987265;N:522345 151 151     764571339 715912069 728730982 828987265 522345 SRX6748559 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.87838 0.89181 0.08908 0.06618 0.7484 0.7485 0.53115 0.59993 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53699 53699 SRR10010380 SRX6748558 SRS5298721 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf wildtype   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf wild type 1 35dpf wild type 1 35dpf wild type 1 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1_35day_WT-1_combined_R1.fq.gz nr5a1_35day_WT-1_combined_R2.fq.gz fastq fastq 3598780584.0 11916492.0 nr5a1 35day WT 1 combined R1.fq.gz 0:151 1:151 A:886857565;C:874550481;G:894991137;T:941808129;N:573272 151 151     886857565 874550481 894991137 941808129 573272 SRX6748558 SRS5298721 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.9139 0.92164 0.10525 0.06463 0.75057 0.75211 0.49642 0.57074 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53700 53700 SRR10010381 SRX6748557 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 6 35dpf nr5a1b mutant 6 35dpf nr5a1b mutant 6 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-6_combined_R1.fq.gz nr5a1b35dmut-6_combined_R2.fq.gz fastq fastq 4476352418.0 14822359.0 nr5a1b35dmut 6 combined R1.fq.gz 0:151 1:151 A:1120206233;C:1067519728;G:1089929887;T:1197971503;N:725067 151 151     1120206233 1067519728 1089929887 1197971503 725067 SRX6748557 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91501 0.91912 0.08509 0.05807 0.74663 0.7488 0.51898 0.57667 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53701 53701 SRR10010382 SRX6748556 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 5 35dpf nr5a1b mutant 5 35dpf nr5a1b mutant 5 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-5_combined_R1.fq.gz nr5a1b35dmut-5_combined_R2.fq.gz fastq fastq 4009328142.0 13275921.0 nr5a1b35dmut 5 combined R1.fq.gz 0:151 1:151 A:1067904920;C:901186174;G:923523205;T:1116013227;N:700616 151 151     1067904920 901186174 923523205 1116013227 700616 SRX6748556 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.80761 0.83261 0.06793 0.05143 0.75911 0.76114 0.55479 0.61755 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53704 53704 SRR10010385 SRX6748553 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 6 35dpf nr5a1a mutant 6 35dpf nr5a1a mutant 6 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-6_combined_R1.fq.gz nr5a1a35dmut-6_combined_R2.fq.gz fastq fastq 3073492354.0 10177127.0 nr5a1a35dmut 6 combined R1.fq.gz 0:151 1:151 A:789160217;C:716824009;G:740200723;T:826797684;N:509721 151 151     789160217 716824009 740200723 826797684 509721 SRX6748553 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.87516 0.88431 0.09065 0.07016 0.74588 0.74726 0.53057 0.60951 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53705 53705 SRR10010386 SRX6748552 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 5 35dpf nr5a1a mutant 5 35dpf nr5a1a mutant 5 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-5_combined_R1.fq.gz nr5a1a35dmut-5_combined_R2.fq.gz fastq fastq 3240379668.0 10729734.0 nr5a1a35dmut 5 combined R1.fq.gz 0:151 1:151 A:850546438;C:745212890;G:765395973;T:878658019;N:566348 151 151     850546438 745212890 765395973 878658019 566348 SRX6748552 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.81872 0.83649 0.07435 0.05495 0.75225 0.75461 0.51257 0.58856 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53707 53707 SRR10010388 SRX6748550 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 2 35dpf nr5a1a mutant 2 35dpf nr5a1a mutant 2 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-2_combined_R1.fq.gz nr5a1a35dmut-2_combined_R2.fq.gz fastq fastq 1239380518.0 4103909.0 nr5a1a35dmut 2 combined R1.fq.gz 0:151 1:151 A:309089709;C:300159914;G:303434072;T:326498923;N:197900 151 151     309089709 300159914 303434072 326498923 197900 SRX6748550 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91546 0.92068 0.11935 0.07796 0.74397 0.7474 0.48962 0.61439 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53708 53708 SRR10010389 SRX6748549 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 1 35dpf nr5a1a mutant 1 35dpf nr5a1a mutant 1 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-1_combined_R1.fq.gz nr5a1a35dmut-1_combined_R2.fq.gz fastq fastq 2224834906.0 7367003.0 nr5a1a35dmut 1 combined R1.fq.gz 0:151 1:151 A:541266079;C:545117817;G:559850378;T:578249036;N:351596 151 151     541266079 545117817 559850378 578249036 351596 SRX6748549 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91337 0.9214 0.12797 0.08298 0.74961 0.75483 0.45923 0.54594 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53709 53709 SRR10010390 SRX6748548 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 4 35dpf nr5a1a mutant 4 35dpf nr5a1a mutant 4 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-4_combined_R1.fq.gz nr5a1a35dmut-4_combined_R2.fq.gz fastq fastq 2564347836.0 8491218.0 nr5a1a35dmut 4 combined R1.fq.gz 0:151 1:151 A:626506801;C:604109158;G:622843659;T:710461729;N:426489 151 151     626506801 604109158 622843659 710461729 426489 SRX6748548 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.88743 0.91434 0.08038 0.05675 0.75562 0.75676 0.47736 0.57787 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53710 53710 SRR10010391 SRX6748547 SRS5298719 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a mutant 3 35dpf nr5a1a mutant 3 35dpf nr5a1a mutant 3 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1a35dmut-3_combined_R1.fq.gz nr5a1a35dmut-3_combined_R2.fq.gz fastq fastq 2109532212.0 6985206.0 nr5a1a35dmut 3 combined R1.fq.gz 0:151 1:151 A:523059463;C:502631876;G:510494846;T:572988523;N:357504 151 151     523059463 502631876 510494846 572988523 357504 SRX6748547 SRS5298719 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.89446 0.90702 0.08692 0.06146 0.75049 0.75312 0.5212 0.57721 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53715 53715 SRR10010396 SRX6748542 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 13 35dpf nr5a1a nr5a1b double mutant 13 35dpf nr5a1a nr5a1b double mutant 13 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-13_combined_R1.fq.gz nr5a1ab35dmut-13_combined_R2.fq.gz fastq fastq 4623122002.0 15308351.0 nr5a1ab35dmut 13 combined R1.fq.gz 0:151 1:151 A:1157235877;C:1116162876;G:1129874932;T:1219134272;N:714045 151 151     1157235877 1116162876 1129874932 1219134272 714045 SRX6748542 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.91894 0.92533 0.11425 0.08034 0.75635 0.76023 0.50951 0.61492 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53716 53716 SRR10010397 SRX6748541 SRS5298717 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1a nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 12 35dpf nr5a1a nr5a1b double mutant 12 35dpf nr5a1a nr5a1b double mutant 12 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1ab35dmut-12_combined_R1.fq.gz nr5a1ab35dmut-12_combined_R2.fq.gz fastq fastq 2610452666.0 8643883.0 nr5a1ab35dmut 12 combined R1.fq.gz 0:151 1:151 A:648839778;C:629525229;G:642133919;T:689532605;N:421135 151 151     648839778 629525229 642133919 689532605 421135 SRX6748541 SRS5298717 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90931 0.91675 0.11029 0.07732 0.74584 0.74937 0.48342 0.59544 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
53717 53717 SRR10010398 SRX6748540 SRS5298716 SRP219014 PRJNA561212 RNA Seq of nr5a1a and nr5a1b mutant zebrafish PRJNA561212 Transcriptome Analysis Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.         35dpf nr5a1b   strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 35dpf nr5a1b mutant 3 35dpf nr5a1b mutant 3 35dpf nr5a1b mutant 3 Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 4000   SRP219014     nr5a1b35dmut-3_combined_R1.fq.gz nr5a1b35dmut-3_combined_R2.fq.gz fastq fastq 1943393556.0 6435078.0 nr5a1b35dmut 3 combined R1.fq.gz 0:151 1:151 A:475436905;C:468830275;G:477482918;T:521312410;N:331048 151 151     475436905 468830275 477482918 521312410 331048 SRX6748540 SRS5298716 SRA946180 University of Oregon|Institute of Neuroscience University of Oregon 2 0.90426 0.92131 0.09556 0.06323 0.75327 0.75292 0.50371 0.57748 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-08-21 Juvenile Juvenile Trunk Surface Structure
62742 62742 SRR13360748 SRX9785053 SRS7972286 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM2 PM2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm2_S8_R1_001.fastq.gz fastq 3517898944.0 46288144.0 pm2 S8 R1 001.fastq.gz 0:76 1:0 A:914616261;C:828363626;G:805674434;T:969167482;N:77141 76 0     914616261 828363626 805674434 969167482 77141 SRX9785053 SRS7972286 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.94008   0.0747   0.71394   0.51572   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62743 62743 SRR13360749 SRX9785052 SRS7972285 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM1 PM1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm1_S7_R1_001.fastq.gz fastq 1974822380.0 25984505.0 pm1 S7 R1 001.fastq.gz 0:76 1:0 A:561606319;C:416363486;G:408486827;T:588324386;N:41362 76 0     561606319 416363486 408486827 588324386 41362 SRX9785052 SRS7972285 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.9274   0.16109   0.74351   0.57108   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62744 62744 SRR13360750 SRX9785051 SRS7972284 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP4 CP4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp4_S4_R1_001.fastq.gz fastq 2913402316.0 38334241.0 cp4 S4 R1 001.fastq.gz 0:76 1:0 A:791131658;C:648321809;G:621173454;T:852725371;N:50024 76 0     791131658 648321809 621173454 852725371 50024 SRX9785051 SRS7972284 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93191   0.1275   0.7333   0.55298   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62745 62745 SRR13360751 SRX9785050 SRS7972283 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP3 CP3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp3_S6_R1_001.fastq.gz fastq 2648220684.0 34845009.0 cp3 S6 R1 001.fastq.gz 0:76 1:0 A:697194378;C:597685138;G:585283565;T:767999519;N:58084 76 0     697194378 597685138 585283565 767999519 58084 SRX9785050 SRS7972283 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93629   0.1048   0.7349   0.54364   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62746 62746 SRR13360752 SRX9785049 SRS7972282 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP2 CP2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp2_S5_R1_001.fastq.gz fastq 2339410872.0 30781722.0 cp2 S5 R1 001.fastq.gz 0:76 1:0 A:620056592;C:539298564;G:520500416;T:659503250;N:52050 76 0     620056592 539298564 520500416 659503250 52050 SRX9785049 SRS7972282 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93909   0.0916   0.70942   0.51709   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62747 62747 SRR13360753 SRX9785048 SRS7972281 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP1 CP1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp1_S4_R1_001.fastq.gz fastq 2271445592.0 29887442.0 cp1 S4 R1 001.fastq.gz 0:76 1:0 A:620595380;C:508382666;G:499686333;T:642731924;N:49289 76 0     620595380 508382666 499686333 642731924 49289 SRX9785048 SRS7972281 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93497   0.1129   0.71127   0.50787   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62748 62748 SRR13360754 SRX9785047 SRS7972280 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ4 CZ4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz4_S1_R1_001.fastq.gz fastq 2772612848.0 36481748.0 cz4 S1 R1 001.fastq.gz 0:76 1:0 A:753409223;C:625962831;G:590503241;T:802690640;N:46913 76 0     753409223 625962831 590503241 802690640 46913 SRX9785047 SRS7972280 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.92942   0.15362   0.62889   0.51867   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62749 62749 SRR13360755 SRX9785046 SRS7972279 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ3 CZ3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz3_S3_R1_001.fastq.gz fastq 2424287672.0 31898522.0 cz3 S3 R1 001.fastq.gz 0:76 1:0 A:629966430;C:571438897;G:558947157;T:663881953;N:53235 76 0     629966430 571438897 558947157 663881953 53235 SRX9785046 SRS7972279 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.94199   0.04836   0.72218   0.48478   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62750 62750 SRR13360756 SRX9785045 SRS7972278 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM4 PM4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm4_S7_R1_001.fastq.gz fastq 2901513560.0 38177810.0 pm4 S7 R1 001.fastq.gz 0:76 1:0 A:737189471;C:698799076;G:664901115;T:800575145;N:48753 76 0     737189471 698799076 664901115 800575145 48753 SRX9785045 SRS7972278 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.95173   0.04367   0.74089   0.50116   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62751 62751 SRR13360757 SRX9785044 SRS7972277 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM3 PM3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm3_S9_R1_001.fastq.gz fastq 3148390744.0 41426194.0 pm3 S9 R1 001.fastq.gz 0:76 1:0 A:834545372;C:725073648;G:704241250;T:884462724;N:67750 76 0     834545372 725073648 704241250 884462724 67750 SRX9785044 SRS7972277 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.94256   0.09248   0.72099   0.52303   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62752 62752 SRR13360758 SRX9785043 SRS7972276 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ2 CZ2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz2_S2_R1_001.fastq fastq 2207708116.0 29048791.0 cz2 S2 R1 001.fastq 0:76 1:0 A:614048827;C:488071931;G:474165427;T:631372646;N:49285 76 0     614048827 488071931 474165427 631372646 49285 SRX9785043 SRS7972276 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93271   0.12538   0.71733   0.53166   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62753 62753 SRR13360759 SRX9785042 SRS7972275 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ1 CZ1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz1_S1_R1_001.fastq.gz fastq 2264115696.0 29790996.0 cz1 S1 R1 001.fastq.gz 0:76 1:0 A:619936364;C:496981021;G:501038961;T:646109550;N:49800 76 0     619936364 496981021 501038961 646109550 49800 SRX9785042 SRS7972275 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93737   0.1307   0.73003   0.55416   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
68893 68893 SRR18218072 SRX14364503 SRS12177798 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Tu AB mMyc 7   strain:Tu/AB|age:41 days|sex:not collected|tissue:lymphoid|birth date:04 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB Tu AB mMyc 7 Tu AB mMyc 7 Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAXRAAPEI-P87H3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAXRAAPEI-P87H3_2.fq.gz fastq fastq 18002105400.0 60007018.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAXRAAPEI P87H3 1.fq.gz 0:150 1:150 A:4483057959;C:4549819065;G:4562924506;T:4406277865;N:26005 150 150     4483057959 4549819065 4562924506 4406277865 26005 SRX14364503 SRS12177798 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.9259 0.92681 0.09642 0.09697 0.82479 0.82546 0.50634 0.5148 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Juvenile Juvenile Lymphatic System Cardiovascular System
68894 68894 SRR18218073 SRX14364502 SRS12177797 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Tu AB mMyc 6   strain:Tu/AB|age:42 days|sex:not collected|tissue:lymphoid|birth date:03 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB Tu AB mMyc 6 Tu AB mMyc 6 Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAWRABPEI-P75G3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAWRABPEI-P75G3_2.fq.gz fastq fastq 18085463400.0 60284878.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAWRABPEI P75G3 1.fq.gz 0:150 1:150 A:4716166539;C:4371919988;G:4399782048;T:4597568953;N:25872 150 150     4716166539 4371919988 4399782048 4597568953 25872 SRX14364502 SRS12177797 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.90432 0.90596 0.06444 0.06367 0.80048 0.80095 0.51671 0.51624 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Juvenile Juvenile Lymphatic System Cardiovascular System
68895 68895 SRR18218074 SRX14364501 SRS12177796 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Tu AB mMyc 5   strain:Tu/AB|age:42 days|sex:not collected|tissue:lymphoid|birth date:03 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB Tu AB mMyc 5 Tu AB mMyc 5 Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAVRAAPEI-P63F3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAVRAAPEI-P63F3_2.fq.gz fastq fastq 18063312600.0 60211042.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAVRAAPEI P63F3 1.fq.gz 0:150 1:150 A:4440821008;C:4618318980;G:4635597240;T:4368548938;N:26434 150 150     4440821008 4618318980 4635597240 4368548938 26434 SRX14364501 SRS12177796 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.91708 0.91735 0.0319 0.0316 0.80793 0.80744 0.50004 0.5071 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Juvenile Juvenile Lymphatic System Cardiovascular System
68898 68898 SRR18218077 SRX14364498 SRS12177793 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Tu AB mMyc+P1mut 6   strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB Tu AB mMyc+P1mut 6 Tu AB mMyc+P1mut 6 Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEABARAAPEI-P28C4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEABARAAPEI-P28C4_2.fq.gz fastq fastq 18034321800.0 60114406.0 FCHT5GHDSXX L1 HKRDZEBmfpEABARAAPEI P28C4 1.fq.gz 0:150 1:150 A:4518122158;C:4519676234;G:4543758117;T:4452738564;N:26727 150 150     4518122158 4519676234 4543758117 4452738564 26727 SRX14364498 SRS12177793 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.94431 0.94437 0.10494 0.10462 0.83177 0.83037 0.51143 0.51642 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Juvenile Juvenile Lymphatic System Cardiovascular System
68899 68899 SRR18218078 SRX14364497 SRS12177792 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Tu AB mMyc+P1mut 5   strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB Tu AB mMyc+P1mut 5 Tu AB mMyc+P1mut 5 Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAZRAAPEI-P16B4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAZRAAPEI-P16B4_2.fq.gz fastq fastq 17750634300.0 59168781.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAZRAAPEI P16B4 1.fq.gz 0:150 1:150 A:4503506819;C:4398697723;G:4432972998;T:4415430837;N:25923 150 150     4503506819 4398697723 4432972998 4415430837 25923 SRX14364497 SRS12177792 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.94306 0.94321 0.07511 0.0748 0.79837 0.79819 0.51326 0.50902 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Juvenile Juvenile Lymphatic System Cardiovascular System
68900 68900 SRR18218079 SRX14364496 SRS12177791 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Tu AB mMyc+P1mut 4   strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB Tu AB mMyc+P1mut 4 Tu AB mMyc+P1mut 4 Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAYRAAPEI-P4A4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAYRAAPEI-P4A4_2.fq.gz fastq fastq 18063110700.0 60210369.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAYRAAPEI P4A4 1.fq.gz 0:150 1:150 A:4583950532;C:4496933352;G:4489104841;T:4493095718;N:26257 150 150     4583950532 4496933352 4489104841 4493095718 26257 SRX14364496 SRS12177791 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.95231 0.9534 0.12525 0.12554 0.84404 0.84323 0.52132 0.53078 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Juvenile Juvenile Lymphatic System Cardiovascular System

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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");;