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run_metadata

143 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation = "Trunk"

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experiment.library_selection 7

devstage_curation 7

devstage_curation_coarse 5

experiment.library_strategy 4

experiment.platform 3

tissue_curation_coarse 1

tissue_curation 1

  • Trunk · 143 ✖

technology 1

  • unknown · 143 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 143 ✖
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
125 125 DRR189379 DRX179844 DRS200410 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 3 SAMD00182222   sample name:Emx3 Larva body 3|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182222 DRX179844 Emx3 / Larva body 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182222       1759409208.0 48872478.0 DRR189379 0:36 A:401147348;C:424523813;G:426350919;T:507310828;N:76300 36       401147348 424523813 426350919 507310828 76300 DRX179844 DRS200410 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90975   0.11439   0.66076   0.47775   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
126 126 DRR189378 DRX179843 DRS200409 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 2 SAMD00182221   sample name:Emx3 Larva body 2|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182221 DRX179843 Emx3 / Larva body 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182221       1318201020.0 36616695.0 DRR189378 0:36 A:297850068;C:316786585;G:323717530;T:379789606;N:57231 36       297850068 316786585 323717530 379789606 57231 DRX179843 DRS200409 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.9116   0.11269   0.65837   0.46733   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
127 127 DRR189377 DRX179842 DRS200408 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 1 SAMD00182220   sample name:Emx3 Larva body 1|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182220 DRX179842 Emx3 / Larva body 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182220       812483964.0 22568999.0 DRR189377 0:36 A:185173338;C:197790160;G:197482964;T:232000884;N:36618 36       185173338 197790160 197482964 232000884 36618 DRX179842 DRS200408 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91107   0.1171   0.65981   0.47458   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
128 128 DRR189376 DRX179841 DRS200449 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 3 SAMD00182219   sample name:WT Larva body 3|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182219 DRX179841 WT Larva body 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182219       4030038144.0 111945504.0 DRR189376 0:36 A:943709984;C:971756680;G:977594500;T:1136798448;N:178532 36       943709984 971756680 977594500 1136798448 178532 DRX179841 DRS200449 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89574   0.12331   0.65831   0.48096   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
129 129 DRR189375 DRX179840 DRS200448 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 2 SAMD00182218   sample name:WT Larva body 2|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182218 DRX179840 WT Larva body 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182218       1991670804.0 55324189.0 DRR189375 0:36 A:454367176;C:479012055;G:488407231;T:569793674;N:90668 36       454367176 479012055 488407231 569793674 90668 DRX179840 DRS200448 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90911   0.12455   0.65494   0.47971   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
130 130 DRR189374 DRX179839 DRS200447 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 1 SAMD00182217   sample name:WT Larva body 1|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182217 DRX179839 WT Larva body 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182217       1018340100.0 28287225.0 DRR189374 0:36 A:233370050;C:244140659;G:247795084;T:292989542;N:44765 36       233370050 244140659 247795084 292989542 44765 DRX179839 DRS200447 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91078   0.12578   0.6524   0.48016   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
173 173 DRR075397 DRX069311 DRS075492 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The remaining part of body of control fish 7dpf Control body SAMD00065411   sample name:1 control body 150701 Hiseq3A l3 017|tissue type:Body                 Illumina HiSeq 2500 sequencing of SAMD00065411 DRX069311 Control body 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065411       2653100352.0 73697232.0 DRR075397 0:36 A:656791658;C:620507513;G:625038612;T:750671135;N:91434 36       656791658 620507513 625038612 750671135 91434 DRX069311 DRS075492 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.89666   0.15749   0.67048   0.47755   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Trunk Surface Structure
32541 32541 SRR29303120 SRX24820197 SRS21534299 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L6H 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 10|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L6H 1 L6H 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L6H_1.fq.gz fastq 619966455.0 12156205.0 L6H 1.fq.gz 0:51 A:143411079;C:162001488;G:168382605;T:146007422;N:163861 51       143411079 162001488 168382605 146007422 163861 SRX24820197 SRS21534299 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01303   0.00337   0.99472   0.5628   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32542 32542 SRR29303121 SRX24820196 SRS21534298 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L3H 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 09|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L3H 3 L3H 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L3H_3.fq.gz fastq 738125703.0 14473053.0 L3H 3.fq.gz 0:51 A:176614297;C:190760467;G:197157923;T:173400138;N:192878 51       176614297 190760467 197157923 173400138 192878 SRX24820196 SRS21534298 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01163   0.00356   0.99379   0.55469   51   T   under 1.2% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32543 32543 SRR29303122 SRX24820195 SRS21534297 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L3H 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 08|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L3H 2 L3H 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L3H_2.fq.gz fastq 489154821.0 9591271.0 L3H 2.fq.gz 0:51 A:109695797;C:132121151;G:127787221;T:119539033;N:11619 51       109695797 132121151 127787221 119539033 11619 SRX24820195 SRS21534297 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.05359   0.01132   0.98924   0.55364   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32544 32544 SRR29303123 SRX24820194 SRS21534296 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L3H 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 07|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L3H 1 L3H 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L3H_1.fq.gz fastq 551502015.0 10813765.0 L3H 1.fq.gz 0:51 A:130437158;C:141969110;G:146479841;T:132605147;N:10759 51       130437158 141969110 146479841 132605147 10759 SRX24820194 SRS21534296 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.13403   0.01834   0.98735   0.54849   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32545 32545 SRR29303124 SRX24820193 SRS21534295 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L1H 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 06|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L1H 3 L1H 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L1H_3.fq.gz fastq 524533827.0 10284977.0 L1H 3.fq.gz 0:51 A:118598837;C:136729611;G:142993590;T:126201873;N:9916 51       118598837 136729611 142993590 126201873 9916 SRX24820193 SRS21534295 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.00829   0.00187   0.99472   0.54701   51   T   under 1.2% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32546 32546 SRR29303125 SRX24820192 SRS21534294 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L1H 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 05|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L1H 2 L1H 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L1H_2.fq.gz fastq 541697163.0 10621513.0 L1H 2.fq.gz 0:51 A:126751483;C:135818134;G:141122995;T:137953543;N:51008 51       126751483 135818134 141122995 137953543 51008 SRX24820192 SRS21534294 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.33438   0.08101   0.98238   0.53337   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32547 32547 SRR29303126 SRX24820191 SRS21534293 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L1H 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 04|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L1H 1 L1H 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L1H_1.fq.gz fastq 930096282.0 18237182.0 L1H 1.fq.gz 0:51 A:212568445;C:243497911;G:260145458;T:213851032;N:33436 51       212568445 243497911 260145458 213851032 33436 SRX24820191 SRS21534293 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.64143   0.02683   0.98683   0.5342   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32548 32548 SRR29303127 SRX24820190 SRS21534292 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         DD 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 03|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae DD 3 DD 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     DD_3.fq.gz fastq 667459389.0 13087439.0 DD 3.fq.gz 0:51 A:157267065;C:168909886;G:178336724;T:162865168;N:80546 51       157267065 168909886 178336724 162865168 80546 SRX24820190 SRS21534292 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.19375   0.03528   0.98827   0.55124   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32549 32549 SRR29303128 SRX24820189 SRS21534291 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L6H 3 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 12|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L6H 3 L6H 3 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L6H_3.fq.gz fastq 551181072.0 10807472.0 L6H 3.fq.gz 0:51 A:126813056;C:141881980;G:147676363;T:134665008;N:144665 51       126813056 141881980 147676363 134665008 144665 SRX24820189 SRS21534291 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.09301   0.01507   0.99042   0.54323   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32550 32550 SRR29303129 SRX24820188 SRS21534290 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         L6H 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 11|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae L6H 2 L6H 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     L6H_2.fq.gz fastq 571762632.0 11211032.0 L6H 2.fq.gz 0:51 A:138521192;C:148068464;G:150615597;T:134408189;N:149190 51       138521192 148068464 150615597 134408189 149190 SRX24820188 SRS21534290 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01523   0.00336   0.9933   0.57685   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32551 32551 SRR29303130 SRX24820187 SRS21534289 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         DD 2 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 02|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae DD 2 DD 2 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     DD_2.fq.gz fastq 706940937.0 13861587.0 DD 2.fq.gz 0:51 A:162899595;C:189209828;G:187422113;T:167222837;N:186564 51       162899595 189209828 187422113 167222837 186564 SRX24820187 SRS21534289 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.02266   0.00566   0.99334   0.56959   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
32552 32552 SRR29303131 SRX24820186 SRS21534288 SRP512097 PRJNA1120592 Light induce Zebrafish larvae PRJNA1120592 Other Light induce Zebrafish larvae miRNA         DD 1 miRNA   breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 01|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA seq of zebrafish larvae DD 1 DD 1 miRNA seq     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE ILLUMINA Illumina HiSeq 3000   SRP512097     DD_1.fq.gz fastq 540332862.0 10594762.0 DD 1.fq.gz 0:51 A:127336994;C:143901414;G:142437491;T:126515166;N:141797 51       127336994 143901414 142437491 126515166 141797 SRX24820186 SRS21534288 SRA1890590 Lanzhou University|College of Life Science Lanzhou University 1 0.01404   0.00313   0.99484   0.56573   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-06-06 Larval Larval Trunk Surface Structure
36272 36272 SRR298567 SRX079845 SRS212651 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   ZiliIPTes GSM727524   tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL ZiliIPTes three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. RNA obtained from immunoprecipitation with Zili antibody   Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Zili antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727524 GSM727524: ZiliIPTes GSM727524: ZiliIPTes GSM727524: ZiliIPTes 1   GEO Accession:GSM727524 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP007331   read name barcode proc directive:ignore ZiliIPTes.fastq fastq 995759064.0 27659974.0 GSM727524 1 0:36   36                 SRX079845 SRS212651 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.0537   0.03117   0.95856   0.42091   36   B   usable mapping rate illumina early_illumina 5prime size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Trunk Surface Structure
36335 36335 SRR398322 SRX115580 SRS285697 SRP010291 PRJNA150927 miR 221 is required for endothelial tip cell behaviors during vascular development GSE35078 Transcriptome Analysis Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.   pubmed:22340502   miRNA GFP minus GSM861784   source name:whole zebrafish embryos at 24 hpf|age:24 hpf|development stage:embryo|tissue:whole body|cell type:all cell types miRNA GFP minus The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. whole zebrafish embryos at 24 hpf Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers.   age:24 hpf|developmental stage:embryo|tissue:whole body|cell type:all cell types GSM861784 GSM861784: miRNA GFP minus; Danio rerio; RNA Seq GSM861784 1 GSM861784: miRNA GFP minus 1   GEO Accession:GSM861784 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP010291     miRNA_CNTL_WT.fastq.gz fastq 295021332.0 8195037.0 GSM861784 r1 0:36 A:70414178;C:53495749;G:76994313;T:87833261;N:6283831 36       70414178 53495749 76994313 87833261 6283831 SRX115580 SRS285697 SRA049243 GEO Nathan Lawson Lab, PGFE, Umass Medical School 1 0.02832   0.02716   0.99957   0.43137   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2012-01-12 Pharyngula Embryo Trunk Surface Structure
40162 40162 SRR2937381 SRX1440089 SRS1170438 SRP066406 PRJNA302080 Danio rerio Raw sequence reads PRJNA302080 Whole Genome Sequencing The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon         T   strain:AB strain|age:0|dev stage:embryo|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon T T cDNA/Total RNA was extracted from 50 homogenized zebrafish embryos treated with and without xxx respectively by using Trizol regent Invitrogen USA according to the manufacturer’s instruction and treated with RNase free DNase I Takara Biotechnology China. RNA integrity was confirmed with a minimum RNA integrated number value of 8 by the 2100 bio analyzer Agilent. PolyA mRNA was enriched with oligo dT beads and then was fragmented. The cleaved RNA fragments were transcribed into first strand cDNA using reverse transcriptase and random hexamer primers which was followed by second strand cDNA synthesis. The double stranded cDNA was further subjected to end repair phosphorylation 3’ adenylation and adaptor ligation in sequence. Adaptor ligated fragments were selected according to the size 250 to 350 bp and the desired range of cDNA fragments were excised from the gel. The fragments were enriched by PCR amplification. The quality and quantity of the two libraries one library was treated with TDF but the other one did not were determined g on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. Subsequently the cDNA library was sequenced on a flow cell using Illumina HiSeq2000.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000 <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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP066406     T.fq.gz fastq 587807332.0 11996068.0 T 0:49 A:146199755;C:143635765;G:149348442;T:148593898;N:29472 49       146199755 143635765 149348442 148593898 29472 SRX1440089 SRS1170438 SRA312474 National Central University|Chen-Ssu-Ching lab National Central University 1 0.95023   0.02672   0.77889   0.46839   49   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Taiwan 2016-11-20 Undetermined Embryo Trunk Surface Structure
40163 40163 SRR2924938 SRX1438257 SRS1168908 SRP066406 PRJNA302080 Danio rerio Raw sequence reads PRJNA302080 Whole Genome Sequencing The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon         D   strain:AB strain|age:0|dev stage:embryo|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon D D cDNA/Total RNA was extracted from 50 homogenized zebrafish embryos treated with and without xxx respectively by using Trizol regent Invitrogen USA according to the manufacturer’s instruction and treated with RNase free DNase I Takara Biotechnology China. RNA integrity was confirmed with a minimum RNA integrated number value of 8 by the 2100 bio analyzer Agilent. PolyA mRNA was enriched with oligo dT beads and then was fragmented. The cleaved RNA fragments were transcribed into first strand cDNA using reverse transcriptase and random hexamer primers which was followed by second strand cDNA synthesis. The double stranded cDNA was further subjected to end repair phosphorylation 3’ adenylation and adaptor ligation in sequence. Adaptor ligated fragments were selected according to the size 250 to 350 bp and the desired range of cDNA fragments were excised from the gel. The fragments were enriched by PCR amplification. The quality and quantity of the two libraries one library was treated with TDF but the other one did not were determined g on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. Subsequently the cDNA library was sequenced on a flow cell using Illumina HiSeq2000.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000 <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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP066406     D.fq.gz fastq 535039673.0 10919177.0 D 0:49 A:135797892;C:127799155;G:132966868;T:138440725;N:35033 49       135797892 127799155 132966868 138440725 35033 SRX1438257 SRS1168908 SRA312306 National Central University|Chen-Ssu-Ching lab National Central University 1 0.93993   0.0586   0.73391   0.46855   49   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Taiwan 2016-11-19 Undetermined Embryo Trunk Surface Structure
41250 41250 SRR3987432 SRX1989729 SRS1593551 SRP080353 PRJNA335856 High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under ß diketone antibiotics exposure to F0 zebrafish GSE85004 Transcriptome Analysis Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day ß diketone antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total 10 117 347 9 818 830 and 12 049 949 raw reads were acquired respectively under the different DKA exposure treatments 0 6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed which included five prime' contaminants those missing the three prime' primer or insert tag sequences with a poly A tail and those shorter than 17 nt and longer than 25 nt. As a result 8 141 146 representing 312 735 unique sequences; control 8 687 210 representing 251 508 unique sequences; 6.25 mg/L and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar and the unique sRNA reads were mainly distributed in the 20 24 nt range among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads respectively. The 22 nt sRNAs were the most abundant with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.       S12 F1 GSM2255739   source name:F1 zebrafish 7 dpf F0 12.5 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:12.5 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf S12 F1 Briefly the raw reads were subjected to the Illumina pipeline filter Solexa 0.3 and then the dataset was further processed with an in house program ACGT101 miR LC Sciences Houston Texas USA to remove adapter dimers junk low complexity common RNA families rRNA tRNA snRNA snoRNA and repeats. Subsequently unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the … F1 zebrafish 7 dpf F0 12.5 mg/L DKA exposure Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon OH USA and used as received: ofluoxacin CAS No. 82419 36 1 purity of 99% ciprofloxacin 85721 33 1 99% enrofloxacin 93106 60 6 99% doxycycline 24390 14 5 99% chlortetracycline 64 72 2 95% and oxytetracycline 79 57 2 99%. Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.   strain/background:AB|genotype/variation:WT|f0 treatment:12.5 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf GSM2255739 GSM2255739: S12 F1; Danio rerio; ncRNA Seq GSM2255739   1 Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol. GEO Accession:GSM2255739 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP080353     S12_F1.fq fastq 602497450.0 12049949.0 GSM2255739 r1 0:50 A:147750395;C:138369661;G:162147841;T:153975593;N:253960 50       147750395 138369661 162147841 153975593 253960 SRX1989729 SRS1593551 SRA446490 GEO Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province 1 0.0   0.0   1.0       50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2016-07-29 Larval Larval Trunk Surface Structure
41251 41251 SRR3987431 SRX1989728 SRS1593550 SRP080353 PRJNA335856 High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under ß diketone antibiotics exposure to F0 zebrafish GSE85004 Transcriptome Analysis Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day ß diketone antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total 10 117 347 9 818 830 and 12 049 949 raw reads were acquired respectively under the different DKA exposure treatments 0 6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed which included five prime' contaminants those missing the three prime' primer or insert tag sequences with a poly A tail and those shorter than 17 nt and longer than 25 nt. As a result 8 141 146 representing 312 735 unique sequences; control 8 687 210 representing 251 508 unique sequences; 6.25 mg/L and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar and the unique sRNA reads were mainly distributed in the 20 24 nt range among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads respectively. The 22 nt sRNAs were the most abundant with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.       S6 F1 GSM2255738   source name:F1 zebrafish 7 dpf F0 6.25 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf S6 F1 Briefly the raw reads were subjected to the Illumina pipeline filter Solexa 0.3 and then the dataset was further processed with an in house program ACGT101 miR LC Sciences Houston Texas USA to remove adapter dimers junk low complexity common RNA families rRNA tRNA snRNA snoRNA and repeats. Subsequently unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the … F1 zebrafish 7 dpf F0 6.25 mg/L DKA exposure Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon OH USA and used as received: ofluoxacin CAS No. 82419 36 1 purity of 99% ciprofloxacin 85721 33 1 99% enrofloxacin 93106 60 6 99% doxycycline 24390 14 5 99% chlortetracycline 64 72 2 95% and oxytetracycline 79 57 2 99%. Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.   strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf GSM2255738 GSM2255738: S6 F1; Danio rerio; ncRNA Seq GSM2255738   1 Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol. GEO Accession:GSM2255738 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP080353     S6_F1.fq fastq 490941500.0 9818830.0 GSM2255738 r1 0:50 A:119942635;C:111532763;G:133144810;T:126303825;N:17467 50       119942635 111532763 133144810 126303825 17467 SRX1989728 SRS1593550 SRA446490 GEO Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province 1 1e-05   0.0   1.0       50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2016-07-29 Larval Larval Trunk Surface Structure
41252 41252 SRR3987430 SRX1989727 SRS1593549 SRP080353 PRJNA335856 High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under ß diketone antibiotics exposure to F0 zebrafish GSE85004 Transcriptome Analysis Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day ß diketone antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total 10 117 347 9 818 830 and 12 049 949 raw reads were acquired respectively under the different DKA exposure treatments 0 6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed which included five prime' contaminants those missing the three prime' primer or insert tag sequences with a poly A tail and those shorter than 17 nt and longer than 25 nt. As a result 8 141 146 representing 312 735 unique sequences; control 8 687 210 representing 251 508 unique sequences; 6.25 mg/L and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar and the unique sRNA reads were mainly distributed in the 20 24 nt range among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads respectively. The 22 nt sRNAs were the most abundant with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.       CON F1 GSM2255737   source name:F1 zebrafish 7 dpf F0 0 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:0 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf CON F1 Briefly the raw reads were subjected to the Illumina pipeline filter Solexa 0.3 and then the dataset was further processed with an in house program ACGT101 miR LC Sciences Houston Texas USA to remove adapter dimers junk low complexity common RNA families rRNA tRNA snRNA snoRNA and repeats. Subsequently unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the … F1 zebrafish 7 dpf F0 0 mg/L DKA exposure Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon OH USA and used as received: ofluoxacin CAS No. 82419 36 1 purity of 99% ciprofloxacin 85721 33 1 99% enrofloxacin 93106 60 6 99% doxycycline 24390 14 5 99% chlortetracycline 64 72 2 95% and oxytetracycline 79 57 2 99%. Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.   strain/background:AB|genotype/variation:WT|f0 treatment:0 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf GSM2255737 GSM2255737: CON F1; Danio rerio; ncRNA Seq GSM2255737   1 Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol. GEO Accession:GSM2255737 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP080353     CON_F1.fq fastq 505867350.0 10117347.0 GSM2255737 r1 0:50 A:123471791;C:114424623;G:138931875;T:129020913;N:18148 50       123471791 114424623 138931875 129020913 18148 SRX1989727 SRS1593549 SRA446490 GEO Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province 1 2e-05   0.0   0.99993   0.66666   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2016-07-29 Larval Larval Trunk Surface Structure
41421 41421 SRR4423115 SRX2245299 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Adult male whole body 94 3 94 3 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0094BC03smallZF.fastq fastq 697814234.0 14408051.0 maleRID0094BC03smallZF.fastq 0:48.43 A:165337411;C:177790468;G:184204311;T:170482044;N:0 48       165337411 177790468 184204311 170482044 0 SRX2245299 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.70426   0.16215   0.91027   0.5459   120   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
41423 41423 SRR4423113 SRX2245297 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish: Adult male whole body 99 5 99 5 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0099BC05LargeZF.fastq fastq 3606425618.0 40350582.0 maleRID0099BC05LargeZF.fastq 0:89.38 A:900873268;C:899774590;G:1079098037;T:726679723;N:0 89       900873268 899774590 1079098037 726679723 0 SRX2245297 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.90069   0.21287   0.95726   0.72186   53   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
41425 41425 SRR4423111 SRX2245295 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Adult male whole body 88 3 88 3 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0088BC03smallZF.fastq fastq 523776538.0 11118832.0 maleRID0088BC03smallZF.fastq 0:47.11 A:123827431;C:133478804;G:138882662;T:127587641;N:0 47       123827431 133478804 138882662 127587641 0 SRX2245295 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.69556   0.16368   0.9093   0.54838   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
41427 41427 SRR4423109 SRX2245293 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Adult male whole body 93 3 93 3 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0093BC03smallZF.fastq fastq 692750598.0 14286031.0 maleRID0093BC03smallZF.fastq 0:48.49 A:164412063;C:176380331;G:182539801;T:169418403;N:0 48       164412063 176380331 182539801 169418403 0 SRX2245293 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.70738   0.16645   0.90948   0.55306   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
42197 42197 SRR5485641 SRX2768777 SRS2152486 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         A 3.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads A 3.0.2 A 3.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_4.A_R1.fastq.gz HI.4096.008.Index_4.A_R1.fastq.gz fastq fastq 2072387100.0 20723871.0 HI.4079.001.Index 4.A R1.fastq.gz 0:100 1:0 A:539231555;C:478779687;G:466992364;T:587014266;N:369228 100 0     539231555 478779687 466992364 587014266 369228 SRX2768777 SRS2152486 SRA557480 Brandon University|Biology Brandon University 1 0.94094   0.13282   0.67566   0.46135   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42198 42198 SRR5485640 SRX2768776 SRS2152485 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         B 3.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads B 3.5.2 B 3.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_5.B_R1.fastq.gz HI.4096.008.Index_5.B_R1.fastq.gz fastq fastq 2236492200.0 22364922.0 HI.4079.001.Index 5.B R1.fastq.gz 0:100 1:0 A:580646206;C:518191209;G:502712894;T:634542622;N:399269 100 0     580646206 518191209 502712894 634542622 399269 SRX2768776 SRS2152485 SRA557480 Brandon University|Biology Brandon University 1 0.94188   0.13073   0.67653   0.4635   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42199 42199 SRR5485639 SRX2768775 SRS2152484 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         C 3.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads C 3.20.2 C 3.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_12.C_R1.fastq.gz HI.4096.008.Index_12.C_R1.fastq.gz fastq fastq 1979628000.0 19796280.0 HI.4079.001.Index 12.C R1.fastq.gz 0:100 1:0 A:519406228;C:453563284;G:442115002;T:564195493;N:347993 100 0     519406228 453563284 442115002 564195493 347993 SRX2768775 SRS2152484 SRA557480 Brandon University|Biology Brandon University 1 0.93946   0.14364   0.6759   0.46247   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42200 42200 SRR5485638 SRX2768774 SRS2152483 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         D 3.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads D 3.0.14 D 3.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_19.D_R1.fastq.gz HI.4096.008.Index_19.D_R1.fastq.gz fastq fastq 1856095600.0 18560956.0 HI.4079.001.Index 19.D R1.fastq.gz 0:100 1:0 A:492424946;C:416504198;G:409645413;T:537196088;N:324955 100 0     492424946 416504198 409645413 537196088 324955 SRX2768774 SRS2152483 SRA557480 Brandon University|Biology Brandon University 1 0.9288   0.15497   0.69232   0.46842   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42201 42201 SRR5485637 SRX2768773 SRS2152481 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         E 3.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads E 3.5.14 E 3.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4096.008.Index_1.E_R1.fastq.gz HI.4079.001.Index_1.E_R1.fastq.gz fastq fastq 2936761500.0 29367615.0 HI.4079.001.Index 1.E R1.fastq.gz 0:100 1:0 A:762661816;C:675701333;G:661832769;T:836033713;N:531869 100 0     762661816 675701333 661832769 836033713 531869 SRX2768773 SRS2152481 SRA557480 Brandon University|Biology Brandon University 1 0.93957   0.12499   0.67714   0.4697   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2017-05-08 Undetermined Multi-stage Trunk Surface Structure
42202 42202 SRR5485636 SRX2768772 SRS2152480 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         F 3.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads F 3.20.14 F 3.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_3.F_R1.fastq.gz HI.4096.008.Index_3.F_R1.fastq.gz fastq fastq 2169884500.0 21698845.0 HI.4079.001.Index 3.F R1.fastq.gz 0:100 1:0 A:566808272;C:496620769;G:487930959;T:618144722;N:379778 100 0     566808272 496620769 487930959 618144722 379778 SRX2768772 SRS2152480 SRA557480 Brandon University|Biology Brandon University 1 0.93678   0.13131   0.67635   0.47972   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42203 42203 SRR5485635 SRX2768771 SRS2152482 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         G 4.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads G 4.0.2 G 4.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_9.G_R1.fastq.gz HI.4096.008.Index_9.G_R1.fastq.gz fastq fastq 2008051800.0 20080518.0 HI.4079.001.Index 9.G R1.fastq.gz 0:100 1:0 A:518304309;C:466602325;G:455957803;T:566834696;N:352667 100 0     518304309 466602325 455957803 566834696 352667 SRX2768771 SRS2152482 SRA557480 Brandon University|Biology Brandon University 1 0.94445   0.12419   0.68201   0.46743   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42204 42204 SRR5485634 SRX2768770 SRS2152479 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         H 4.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads H 4.5.2 H 4.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_8.H_R1.fastq.gz HI.4096.008.Index_8.H_R1.fastq.gz fastq fastq 1908097900.0 19080979.0 HI.4079.001.Index 8.H R1.fastq.gz 0:100 1:0 A:494318032;C:441931870;G:431477592;T:540030651;N:339755 100 0     494318032 441931870 431477592 540030651 339755 SRX2768770 SRS2152479 SRA557480 Brandon University|Biology Brandon University 1 0.94216   0.1306   0.68195   0.45834   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42205 42205 SRR5485633 SRX2768769 SRS2152477 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         I 4.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads I 4.20.2 I 4.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_10.I_R1.fastq.gz HI.4096.008.Index_10.I_R1.fastq.gz fastq fastq 2059931100.0 20599311.0 HI.4079.001.Index 10.I R1.fastq.gz 0:100 1:0 A:536731862;C:475769707;G:462890515;T:584183211;N:355805 100 0     536731862 475769707 462890515 584183211 355805 SRX2768769 SRS2152477 SRA557480 Brandon University|Biology Brandon University 1 0.93561   0.13393   0.68225   0.46489   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42206 42206 SRR5485632 SRX2768768 SRS2152478 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         J 4.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads J 4.0.14 J 4.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_11.J_R1.fastq.gz HI.4096.008.Index_11.J_R1.fastq.gz fastq fastq 2199504800.0 21995048.0 HI.4079.001.Index 11.J R1.fastq.gz 0:100 1:0 A:579625731;C:499663817;G:489173373;T:630657278;N:384601 100 0     579625731 499663817 489173373 630657278 384601 SRX2768768 SRS2152478 SRA557480 Brandon University|Biology Brandon University 1 0.93523   0.13836   0.68655   0.47839   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42207 42207 SRR5485631 SRX2768767 SRS2152475 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         K 4.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads K 4.5.14 K 4.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_20.K_R1.fastq.gz HI.4096.008.Index_20.K_R1.fastq.gz fastq fastq 2154282200.0 21542822.0 HI.4079.001.Index 20.K R1.fastq.gz 0:100 1:0 A:563358732;C:494058898;G:482596638;T:613890813;N:377119 100 0     563358732 494058898 482596638 613890813 377119 SRX2768767 SRS2152475 SRA557480 Brandon University|Biology Brandon University 1 0.93863   0.12932   0.67801   0.46426   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42208 42208 SRR5485630 SRX2768766 SRS2152476 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         L 4.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads L 4.20.14 L 4.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4096.008.Index_22.L_R1.fastq.gz HI.4079.001.Index_22.L_R1.fastq.gz fastq fastq 2702515700.0 27025157.0 HI.4079.001.Index 22.L R1.fastq.gz 0:100 1:0 A:708045960;C:615042366;G:603133757;T:775807969;N:485648 100 0     708045960 615042366 603133757 775807969 485648 SRX2768766 SRS2152476 SRA557480 Brandon University|Biology Brandon University 1 0.93316   0.14421   0.68915   0.47027   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2017-05-08 Undetermined Multi-stage Trunk Surface Structure
42209 42209 SRR5485629 SRX2768765 SRS2152474 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         M 5.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads M 5.0.2 M 5.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_25.M_R1.fastq.gz HI.4096.008.Index_25.M_R1.fastq.gz fastq fastq 1999183400.0 19991834.0 HI.4079.001.Index 25.M R1.fastq.gz 0:100 1:0 A:526344986;C:456726468;G:447467581;T:568292150;N:352215 100 0     526344986 456726468 447467581 568292150 352215 SRX2768765 SRS2152474 SRA557480 Brandon University|Biology Brandon University 1 0.9374   0.14185   0.67665   0.47249   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42210 42210 SRR5485628 SRX2768764 SRS2152473 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         N 5.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads N 5.5.2 N 5.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_21.N_R1.fastq.gz HI.4096.008.Index_21.N_R1.fastq.gz fastq fastq 2097386100.0 20973861.0 HI.4079.001.Index 21.N R1.fastq.gz 0:100 1:0 A:551586521;C:479609380;G:467572413;T:598246436;N:371350 100 0     551586521 479609380 467572413 598246436 371350 SRX2768764 SRS2152473 SRA557480 Brandon University|Biology Brandon University 1 0.93984   0.13949   0.68219   0.46921   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42211 42211 SRR5485627 SRX2768763 SRS2152472 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         O 5.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads O 5.20.2 O 5.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_23.O_R1.fastq.gz HI.4096.008.Index_23.O_R1.fastq.gz fastq fastq 2003835800.0 20038358.0 HI.4079.001.Index 23.O R1.fastq.gz 0:100 1:0 A:529075084;C:456810826;G:444441300;T:573155538;N:353052 100 0     529075084 456810826 444441300 573155538 353052 SRX2768763 SRS2152472 SRA557480 Brandon University|Biology Brandon University 1 0.93635   0.15287   0.67712   0.45807   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42212 42212 SRR5485626 SRX2768762 SRS2152471 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         P 5.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads P 5.0.14 P 5.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_27.P_R1.fastq.gz HI.4096.008.Index_27.P_R1.fastq.gz fastq fastq 1799355500.0 17993555.0 HI.4079.001.Index 27.P R1.fastq.gz 0:100 1:0 A:485156399;C:399414298;G:389730888;T:524733869;N:320046 100 0     485156399 399414298 389730888 524733869 320046 SRX2768762 SRS2152471 SRA557480 Brandon University|Biology Brandon University 1 0.92813   0.15749   0.67943   0.47424   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42213 42213 SRR5485625 SRX2768761 SRS2152470 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         Q 5.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads Q 5.5.14 Q 5.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_2.Q_R1.fastq.gz HI.4096.008.Index_2.Q_R1.fastq.gz fastq fastq 2260494100.0 22604941.0 HI.4079.001.Index 2.Q R1.fastq.gz 0:100 1:0 A:602519260;C:506296484;G:495685951;T:655587703;N:404702 100 0     602519260 506296484 495685951 655587703 404702 SRX2768761 SRS2152470 SRA557480 Brandon University|Biology Brandon University 1 0.92524   0.14979   0.6859   0.47957   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42214 42214 SRR5485624 SRX2768760 SRS2152469 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         R 5.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads R 5.20.14 R 5.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_13.R_R1.fastq.gz HI.4096.008.Index_13.R_R1.fastq.gz fastq fastq 1975297900.0 19752979.0 HI.4079.001.Index 13.R R1.fastq.gz 0:100 1:0 A:527732232;C:440160233;G:430962427;T:576091914;N:351094 100 0     527732232 440160233 430962427 576091914 351094 SRX2768760 SRS2152469 SRA557480 Brandon University|Biology Brandon University 1 0.92785   0.15864   0.6814   0.47773   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42215 42215 SRR5485623 SRX2768759 SRS2152468 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         S 6.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:S 6.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads S 6.0.2 S 6.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_6.S_R1.fastq.gz HI.4096.008.Index_6.S_R1.fastq.gz fastq fastq 2690628500.0 26906285.0 HI.4079.001.Index 6.S R1.fastq.gz 0:100 1:0 A:713021693;C:609779787;G:594591832;T:772745072;N:490116 100 0     713021693 609779787 594591832 772745072 490116 SRX2768759 SRS2152468 SRA557480 Brandon University|Biology Brandon University 1 0.93405   0.15472   0.68505   0.45796   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42216 42216 SRR5485622 SRX2768758 SRS2152466 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         T 6.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads T 6.5.2 T 6.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_15.T_R1.fastq.gz HI.4096.008.Index_15.T_R1.fastq.gz fastq fastq 1949043500.0 19490435.0 HI.4079.001.Index 15.T R1.fastq.gz 0:100 1:0 A:515794596;C:441198348;G:430323928;T:561379111;N:347517 100 0     515794596 441198348 430323928 561379111 347517 SRX2768758 SRS2152466 SRA557480 Brandon University|Biology Brandon University 1 0.93579   0.16207   0.68473   0.44993   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42217 42217 SRR5485621 SRX2768757 SRS2152467 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         U 6.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads U 6.20.2 U 6.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_7.U_R1.fastq.gz HI.4096.008.Index_7.U_R1.fastq.gz fastq fastq 1754851900.0 17548519.0 HI.4079.001.Index 7.U R1.fastq.gz 0:100 1:0 A:464191451;C:397313933;G:387262108;T:505777499;N:306909 100 0     464191451 397313933 387262108 505777499 306909 SRX2768757 SRS2152467 SRA557480 Brandon University|Biology Brandon University 1 0.93016   0.16163   0.68329   0.47088   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42218 42218 SRR5485620 SRX2768756 SRS2152463 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         V 6.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads V 6.0.14 V 6.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_18.V_R1.fastq.gz HI.4096.008.Index_18.V_R1.fastq.gz fastq fastq 2027423200.0 20274232.0 HI.4079.001.Index 18.V R1.fastq.gz 0:100 1:0 A:542440452;C:449399743;G:440389586;T:594839784;N:353635 100 0     542440452 449399743 440389586 594839784 353635 SRX2768756 SRS2152463 SRA557480 Brandon University|Biology Brandon University 1 0.92441   0.16974   0.6842   0.48209   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42219 42219 SRR5485619 SRX2768755 SRS2152464 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         W 6.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads W 6.5.14 W 6.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_14.W_R1.fastq.gz HI.4096.008.Index_14.W_R1.fastq.gz fastq fastq 2139528300.0 21395283.0 HI.4079.001.Index 14.W R1.fastq.gz 0:100 1:0 A:569259910;C:478055273;G:469309420;T:622525486;N:378211 100 0     569259910 478055273 469309420 622525486 378211 SRX2768755 SRS2152464 SRA557480 Brandon University|Biology Brandon University 1 0.92551   0.15358   0.68136   0.47093   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42220 42220 SRR5485618 SRX2768754 SRS2152465 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         X 6.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads X 6.20.14 X 6.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_16.X_R1.fastq.gz HI.4096.008.Index_16.X_R1.fastq.gz fastq fastq 1768110400.0 17681104.0 HI.4079.001.Index 16.X R1.fastq.gz 0:100 1:0 A:472810124;C:392555880;G:382616900;T:519817796;N:309700 100 0     472810124 392555880 382616900 519817796 309700 SRX2768754 SRS2152465 SRA557480 Brandon University|Biology Brandon University 1 0.92486   0.16073   0.69041   0.48403   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
47611 47611 SRR6671794 SRX3648486 SRS2913085 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         PBS2   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Control innoculated with PBS|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: uninffected PBS2 PBS2 Total RNA isolated from uninfected abdominal tissue was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     PBS2_GCCAAT_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 792892359.0 15546909.0 PBS2 GCCAAT L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:207417646;C:188867370;G:187996499;T:208448675;N:162169 51       207417646 188867370 187996499 208448675 162169 SRX3648486 SRS2913085 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.92826   0.02642   0.72815   0.45776   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
47612 47612 SRR6671795 SRX3648485 SRS2913084 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         RDRZ   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Infected with Mucor circinelloides spores|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: infected with Mucor circinelloides RDRZ RDRZ Total RNA isolated from abdominal tissue infected with Mucor circinelloides was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     RDRZ_TGACCA_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 741005418.0 14529518.0 RDRZ TGACCA L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:192330774;C:178252917;G:175501754;T:194766886;N:153087 51       192330774 178252917 175501754 194766886 153087 SRX3648485 SRS2913084 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.91685   0.03703   0.70873   0.49947   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
48054 48054 SRR7008006 SRX3940581 SRS3171382 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     MO26h rep1 MO26h 1 Sample3   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 1|BioSampleModel:Model organism or animal                 RNA seq of fsd1 morphants1 MO26h 1 MO26h 1 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     MO26h_1_1.fq.gz fastq 1193983450.0 23879669.0 MO26h 1 1.fq.gz 0:50 A:313344068;C:282899939;G:291404437;T:306051122;N:283884 50       313344068 282899939 291404437 306051122 283884 SRX3940581 SRS3171382 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.95658   0.07921   0.70307   0.47586   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
48055 48055 SRR7008007 SRX3940580 SRS3171381 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     MO26h rep2 MO26h 2 Sample4   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 2|BioSampleModel:Model organism or animal                 RNA seq of fsd1 morphants2 MO26h 2 MO26h 2 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     MO26h_2_1.fq.gz fastq 1199524600.0 23990492.0 MO26h 2 1.fq.gz 0:50 A:318726410;C:282721669;G:287606979;T:310182197;N:287345 50       318726410 282721669 287606979 310182197 287345 SRX3940580 SRS3171381 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.9541   0.08695   0.70404   0.47195   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
48056 48056 SRR7008008 SRX3940579 SRS3171379 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     WT26h rep1 WT26h 1 Sample1   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 1|BioSampleModel:Model organism or animal                 RNA seq of normal embryos1 WT26h 1 WT26h 1 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     WT26h_1_1.fq.gz fastq 1200268650.0 24005373.0 WT26h 1 1.fq.gz 0:50 A:315743815;C:284447849;G:295772915;T:303964473;N:339598 50       315743815 284447849 295772915 303964473 339598 SRX3940579 SRS3171379 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.95659   0.07726   0.70425   0.47269   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
48057 48057 SRR7008009 SRX3940578 SRS3171380 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     WT26h rep2 WT26h 2 Sample2   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 2|BioSampleModel:Model organism or animal                 RNA seq of normal embryos2 WT26h 2 WT26h 2 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     WT26h_2_1.fq.gz fastq 1199179850.0 23983597.0 WT26h 2 1.fq.gz 0:50 A:316605984;C:281184572;G:292581373;T:308419476;N:388445 50       316605984 281184572 292581373 308419476 388445 SRX3940578 SRS3171380 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.95377   0.08617   0.70508   0.4775   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
56303 56303 SRR10916845 SRX7584161 SRS6018089 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 96 hpf GSM4277146   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277146 GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq GSM4277146   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277146 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     A2-43_GTCCGC_L002_R1_001.fastq.gz fastq 2503264497.0 24784797.0 GSM4277146 r1 0:101 1:0 A:610342444;C:605351395;G:584078328;T:703409443;N:82887 101 0     610342444 605351395 584078328 703409443 82887 SRX7584161 SRS6018089 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95646   0.06805   0.69274   0.49865   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56304 56304 SRR10916846 SRX7584161 SRS6018089 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 96 hpf GSM4277146   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277146 GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq GSM4277146   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277146 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     B3-44_CGATGT_L003_R1_001.fastq.gz fastq 2225687409.0 22036509.0 GSM4277146 r2 0:101 1:0 A:543949310;C:537645424;G:518948090;T:625038482;N:106103 101 0     543949310 537645424 518948090 625038482 106103 SRX7584161 SRS6018089 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.9578   0.06735   0.69189   0.49902   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56305 56305 SRR10916847 SRX7584161 SRS6018089 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 96 hpf GSM4277146   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277146 GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq GSM4277146   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277146 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     H3-45_ACTTGA_L003_R1_001.fastq.gz fastq 2597175105.0 25714605.0 GSM4277146 r3 0:101 1:0 A:634560188;C:628995069;G:615407384;T:718090230;N:122234 101 0     634560188 628995069 615407384 718090230 122234 SRX7584161 SRS6018089 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95702   0.06548   0.69333   0.50018   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56306 56306 SRR10916848 SRX7584161 SRS6018089 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 96 hpf GSM4277146   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277146 GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq GSM4277146   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277146 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     F3-46_GCCAAT_L003_R1_001.fastq.gz fastq 2038733480.0 20185480.0 GSM4277146 r4 0:101 1:0 A:496407974;C:493935831;G:480716183;T:567578140;N:95352 101 0     496407974 493935831 480716183 567578140 95352 SRX7584161 SRS6018089 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95838   0.06496   0.69335   0.49217   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56307 56307 SRR10916841 SRX7584160 SRS6018088 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 72 hpf GSM4277145   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277145 GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq GSM4277145   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277145 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     F1-39_AGTTCC_L001_R1_001.fastq.gz fastq 2691303671.0 26646571.0 GSM4277145 r1 0:101 1:0 A:665556474;C:642870170;G:620139397;T:761562504;N:1175126 101 0     665556474 642870170 620139397 761562504 1175126 SRX7584160 SRS6018088 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95083   0.06959   0.68694   0.49115   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56308 56308 SRR10916842 SRX7584160 SRS6018088 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 72 hpf GSM4277145   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277145 GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq GSM4277145   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277145 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     G2-40_ACTGAT_L002_R1_001.fastq.gz fastq 2579165694.0 25536294.0 GSM4277145 r2 0:101 1:0 A:628949965;C:623927227;G:605984325;T:720216822;N:87355 101 0     628949965 623927227 605984325 720216822 87355 SRX7584160 SRS6018088 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95759   0.06521   0.6913   0.49176   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56309 56309 SRR10916843 SRX7584160 SRS6018088 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 72 hpf GSM4277145   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277145 GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq GSM4277145   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277145 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     E1-41_AGTCAA_L001_R1_001.fastq.gz fastq 2601135012.0 25753812.0 GSM4277145 r3 0:101 1:0 A:650835031;C:615158716;G:595000672;T:739001381;N:1139212 101 0     650835031 615158716 595000672 739001381 1139212 SRX7584160 SRS6018088 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.94866   0.07141   0.68887   0.48668   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56310 56310 SRR10916844 SRX7584160 SRS6018088 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 72 hpf GSM4277145   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277145 GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq GSM4277145   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277145 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     A3-42_ATCACG_L003_R1_001.fastq.gz fastq 2214733454.0 21928054.0 GSM4277145 r4 0:101 1:0 A:536220771;C:538941586;G:522287992;T:617178828;N:104277 101 0     536220771 538941586 522287992 617178828 104277 SRX7584160 SRS6018088 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95924   0.06516   0.69061   0.48876   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56311 56311 SRR10916837 SRX7584159 SRS6018087 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 60 hpf GSM4277144   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277144 GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq GSM4277144   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277144 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     G3-35_CAGATC_L003_R1_001.fastq.gz fastq 2118143821.0 20971721.0 GSM4277144 r1 0:101 1:0 A:519832513;C:509799417;G:496904386;T:591508165;N:99340 101 0     519832513 509799417 496904386 591508165 99340 SRX7584159 SRS6018087 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95673   0.07053   0.68753   0.48307   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56312 56312 SRR10916838 SRX7584159 SRS6018087 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 60 hpf GSM4277144   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277144 GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq GSM4277144   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277144 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     E4-36_AGTCAA_L004_R1_001.fastq.gz fastq 2923077966.0 28941366.0 GSM4277144 r2 0:101 1:0 A:716333865;C:709120560;G:684256756;T:813242302;N:124483 101 0     716333865 709120560 684256756 813242302 124483 SRX7584159 SRS6018087 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95832   0.07054   0.69073   0.48784   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56313 56313 SRR10916839 SRX7584159 SRS6018087 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 60 hpf GSM4277144   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277144 GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq GSM4277144   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277144 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     C2-37_GTGGCC_L002_R1_001.fastq.gz fastq 2405094012.0 23812812.0 GSM4277144 r3 0:101 1:0 A:595065779;C:573327677;G:550954965;T:685664326;N:81265 101 0     595065779 573327677 550954965 685664326 81265 SRX7584159 SRS6018087 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95699   0.06973   0.69102   0.49053   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56314 56314 SRR10916840 SRX7584159 SRS6018087 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 60 hpf GSM4277144   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277144 GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq GSM4277144   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277144 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     D3-38_TGACCA_L003_R1_001.fastq.gz fastq 2347133142.0 23238942.0 GSM4277144 r4 0:101 1:0 A:569276409;C:568869930;G:547564379;T:661311262;N:111162 101 0     569276409 568869930 547564379 661311262 111162 SRX7584159 SRS6018087 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95815   0.06396   0.69355   0.48232   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56315 56315 SRR10916833 SRX7584158 SRS6018086 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 48 hpf GSM4277143   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277143 GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq GSM4277143   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277143 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     F2-31_GAGTGG_L002_R1_001.fastq.gz fastq 2619685379.0 25937479.0 GSM4277143 r1 0:101 1:0 A:636766025;C:635045405;G:615398354;T:732386501;N:89094 101 0     636766025 635045405 615398354 732386501 89094 SRX7584158 SRS6018086 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95957   0.06696   0.69075   0.47434   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56316 56316 SRR10916834 SRX7584158 SRS6018086 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 48 hpf GSM4277143   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277143 GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq GSM4277143   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277143 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     C4-32_GGCTAC_L004_R1_001.fastq.gz fastq 2896889676.0 28682076.0 GSM4277143 r2 0:101 1:0 A:718661222;C:694075638;G:664012152;T:820018139;N:122525 101 0     718661222 694075638 664012152 820018139 122525 SRX7584158 SRS6018086 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95619   0.07538   0.6899   0.47621   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56317 56317 SRR10916835 SRX7584158 SRS6018086 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 48 hpf GSM4277143   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277143 GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq GSM4277143   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277143 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     E3-33_ACAGTG_L003_R1_001.fastq.gz fastq 2334977994.0 23118594.0 GSM4277143 r3 0:101 1:0 A:576482393;C:560480528;G:537818737;T:660085376;N:110960 101 0     576482393 560480528 537818737 660085376 110960 SRX7584158 SRS6018086 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95763   0.06915   0.69881   0.47719   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56318 56318 SRR10916836 SRX7584158 SRS6018086 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   BkF 48 hpf GSM4277143   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene BkF 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene GSM4277143 GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq GSM4277143   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277143 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     G4-34_ATGTCA_L004_R1_001.fastq.gz fastq 3090298515.0 30597015.0 GSM4277143 r4 0:101 1:0 A:752311223;C:754003094;G:727487378;T:856366856;N:129964 101 0     752311223 754003094 727487378 856366856 129964 SRX7584158 SRS6018086 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.9593   0.06852   0.69721   0.47942   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56319 56319 SRR10916829 SRX7584157 SRS6018085 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 96 hpf GSM4277142   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO Control 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:1% DMSO GSM4277142 GSM4277142: Control 96 hpf; Danio rerio; RNA Seq GSM4277142   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277142 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     B2-59_GTGAAA_L002_R1_001.fastq.gz fastq 2458252736.0 24339136.0 GSM4277142 r1 0:101 1:0 A:592844538;C:598120714;G:575281979;T:691922086;N:83419 101 0     592844538 598120714 575281979 691922086 83419 SRX7584157 SRS6018085 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95638   0.06618   0.69767   0.46692   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56320 56320 SRR10916830 SRX7584157 SRS6018085 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 96 hpf GSM4277142   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO Control 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:1% DMSO GSM4277142 GSM4277142: Control 96 hpf; Danio rerio; RNA Seq GSM4277142   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277142 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     D2-60_GTTTCG_L002_R1_001.fastq.gz fastq 2624445812.0 25984612.0 GSM4277142 r2 0:101 1:0 A:637941230;C:633570363;G:609402380;T:743443765;N:88074 101 0     637941230 633570363 609402380 743443765 88074 SRX7584157 SRS6018085 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95491   0.06814   0.69455   0.45801   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56321 56321 SRR10916831 SRX7584157 SRS6018085 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 96 hpf GSM4277142   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO Control 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:1% DMSO GSM4277142 GSM4277142: Control 96 hpf; Danio rerio; RNA Seq GSM4277142   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277142 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     F4-61_AGTTCC_L004_R1_001.fastq.gz fastq 2584999050.0 25594050.0 GSM4277142 r3 0:101 1:0 A:630942492;C:629637170;G:606025971;T:718285118;N:108299 101 0     630942492 629637170 606025971 718285118 108299 SRX7584157 SRS6018085 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95797   0.06644   0.69854   0.45736   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56322 56322 SRR10916832 SRX7584157 SRS6018085 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 96 hpf GSM4277142   tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO Control 96 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:96 hpf|treatment:1% DMSO GSM4277142 GSM4277142: Control 96 hpf; Danio rerio; RNA Seq GSM4277142   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277142 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     B1-62_TAGCTT_L001_R1_001.fastq.gz fastq 2330595907.0 23075207.0 GSM4277142 r4 0:101 1:0 A:577282093;C:554550745;G:531987957;T:665756273;N:1018839 101 0     577282093 554550745 531987957 665756273 1018839 SRX7584157 SRS6018085 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95009   0.07667   0.69645   0.45454   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56323 56323 SRR10916825 SRX7584156 SRS6018083 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 72 hpf GSM4277141   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO Control 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:1% DMSO GSM4277141 GSM4277141: Control 72 hpf; Danio rerio; RNA Seq GSM4277141   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277141 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     C1-55_GGCTAC_L001_R1_001.fastq.gz fastq 2503577092.0 24787892.0 GSM4277141 r1 0:101 1:0 A:621449487;C:596176502;G:573313379;T:711542063;N:1095661 101 0     621449487 596176502 573313379 711542063 1095661 SRX7584156 SRS6018083 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.94961   0.07573   0.69485   0.45694   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56324 56324 SRR10916826 SRX7584156 SRS6018083 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 72 hpf GSM4277141   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO Control 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:1% DMSO GSM4277141 GSM4277141: Control 72 hpf; Danio rerio; RNA Seq GSM4277141   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277141 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     A4-56_GATCAG_L004_R1_001.fastq.gz fastq 2734573586.0 27074986.0 GSM4277141 r2 0:101 1:0 A:672128120;C:674528687;G:630293642;T:757509924;N:113213 101 0     672128120 674528687 630293642 757509924 113213 SRX7584156 SRS6018083 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.9596   0.06704   0.70218   0.45451   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56325 56325 SRR10916827 SRX7584156 SRS6018083 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 72 hpf GSM4277141   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO Control 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:1% DMSO GSM4277141 GSM4277141: Control 72 hpf; Danio rerio; RNA Seq GSM4277141   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277141 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     H2-57_ATTCCT_L002_R1_001.fastq.gz fastq 2875677252.0 28472052.0 GSM4277141 r3 0:101 1:0 A:687980848;C:708003051;G:686913934;T:792682658;N:96761 101 0     687980848 708003051 686913934 792682658 96761 SRX7584156 SRS6018083 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95991   0.06385   0.69942   0.46458   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56326 56326 SRR10916828 SRX7584156 SRS6018083 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 72 hpf GSM4277141   tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO Control 72 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:72 hpf|treatment:1% DMSO GSM4277141 GSM4277141: Control 72 hpf; Danio rerio; RNA Seq GSM4277141   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277141 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     G1-58_ATGTCA_L001_R1_001.fastq.gz fastq 2457824799.0 24334899.0 GSM4277141 r4 0:101 1:0 A:586531590;C:602530665;G:582733234;T:684955414;N:1073896 101 0     586531590 602530665 582733234 684955414 1073896 SRX7584156 SRS6018083 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95516   0.06013   0.70092   0.45056   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Larval Larval Trunk Surface Structure
56327 56327 SRR10916821 SRX7584155 SRS6018084 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 60 hpf GSM4277140   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO Control 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:1% DMSO GSM4277140 GSM4277140: Control 60 hpf; Danio rerio; RNA Seq GSM4277140   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277140 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     E2-51_CGTACG_L002_R1_001.fastq.gz fastq 2631272301.0 26052201.0 GSM4277140 r1 0:101 1:0 A:636992903;C:637434881;G:617397859;T:739358160;N:88498 101 0     636992903 637434881 617397859 739358160 88498 SRX7584155 SRS6018084 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95868   0.06185   0.69893   0.45282   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56328 56328 SRR10916822 SRX7584155 SRS6018084 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 60 hpf GSM4277140   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO Control 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:1% DMSO GSM4277140 GSM4277140: Control 60 hpf; Danio rerio; RNA Seq GSM4277140   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277140 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     H4-52_CCGTCC_L004_R1_001.fastq.gz fastq 3099842005.0 30691505.0 GSM4277140 r2 0:101 1:0 A:746424596;C:763800562;G:740203116;T:849281933;N:131798 101 0     746424596 763800562 740203116 849281933 131798 SRX7584155 SRS6018084 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95949   0.06262   0.70283   0.45043   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56329 56329 SRR10916823 SRX7584155 SRS6018084 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 60 hpf GSM4277140   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO Control 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:1% DMSO GSM4277140 GSM4277140: Control 60 hpf; Danio rerio; RNA Seq GSM4277140   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277140 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     H1-53_CCGTCC_L001_R1_001.fastq.gz fastq 2774786534.0 27473134.0 GSM4277140 r3 0:101 1:0 A:660907129;C:687274890;G:662643674;T:762751054;N:1209787 101 0     660907129 687274890 662643674 762751054 1209787 SRX7584155 SRS6018084 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95683   0.05848   0.70191   0.45459   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56330 56330 SRR10916824 SRX7584155 SRS6018084 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 60 hpf GSM4277140   tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO Control 60 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:60 hpf|treatment:1% DMSO GSM4277140 GSM4277140: Control 60 hpf; Danio rerio; RNA Seq GSM4277140   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277140 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     B4-54_TAGCTT_L004_R1_001.fastq.gz fastq 2960262530.0 29309530.0 GSM4277140 r4 0:101 1:0 A:740908620;C:699500257;G:674362882;T:845364000;N:126771 101 0     740908620 699500257 674362882 845364000 126771 SRX7584155 SRS6018084 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95529   0.07342   0.69783   0.45292   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56331 56331 SRR10916817 SRX7584154 SRS6018082 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 48 hpf GSM4277139   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO Control 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:1% DMSO GSM4277139 GSM4277139: Control 48 hpf; Danio rerio; RNA Seq GSM4277139   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277139 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     D4-47_CTTGTA_L004_R1_001.fastq.gz fastq 2845394927.0 28172227.0 GSM4277139 r1 0:101 1:0 A:696407866;C:689539633;G:660246907;T:799078393;N:122128 101 0     696407866 689539633 660246907 799078393 122128 SRX7584154 SRS6018082 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95735   0.07029   0.70094   0.41347   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56332 56332 SRR10916818 SRX7584154 SRS6018082 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 48 hpf GSM4277139   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO Control 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:1% DMSO GSM4277139 GSM4277139: Control 48 hpf; Danio rerio; RNA Seq GSM4277139   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277139 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     D1-48_CTTGTA_L001_R1_001.fastq.gz fastq 2492562638.0 24678838.0 GSM4277139 r2 0:101 1:0 A:614317033;C:596890437;G:569548715;T:710717116;N:1089337 101 0     614317033 596890437 569548715 710717116 1089337 SRX7584154 SRS6018082 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95109   0.06997   0.69635   0.459   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56333 56333 SRR10916819 SRX7584154 SRS6018082 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 48 hpf GSM4277139   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO Control 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:1% DMSO GSM4277139 GSM4277139: Control 48 hpf; Danio rerio; RNA Seq GSM4277139   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277139 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     C3-49_TTAGGC_L003_R1_001.fastq.gz fastq 2323634684.0 23006284.0 GSM4277139 r3 0:101 1:0 A:560892305;C:565585370;G:543493908;T:653554844;N:108257 101 0     560892305 565585370 543493908 653554844 108257 SRX7584154 SRS6018082 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.96012   0.0605   0.70891   0.44674   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
56334 56334 SRR10916820 SRX7584154 SRS6018082 SRP243451 PRJNA602305 Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes. GSE143945 Transcriptome Analysis Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF dibenzo[b k]fluoranthene dibenzo[a h]anthracene and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer BkF. The X fin phenotype was dependent on the AHR paralog Ahr2 and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue where the phenotype was manifest were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48 60 72 and 96 hpf from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files totaling eight processed samples.   pubmed:32384158   Control 48 hpf GSM4277139   tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO Control 48 hpf Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition. Distal trunk tissue Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil plates were placed on an automated shaker overnight at 28.5˚C. Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure wells were covered in parafilm and animals were maintained in the dark at 28.5˚C. developmental stage:48 hpf|treatment:1% DMSO GSM4277139 GSM4277139: Control 48 hpf; Danio rerio; RNA Seq GSM4277139   1 Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. GEO Accession:GSM4277139 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP243451     A1-50_GATCAG_L001_R1_001.fastq.gz fastq 2247754394.0 22254994.0 GSM4277139 r4 0:101 1:0 A:566228379;C:548437322;G:509638046;T:622507773;N:942874 101 0     566228379 548437322 509638046 622507773 942874 SRX7584154 SRS6018082 SRA1028878 GEO Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University 1 0.95297   0.06518   0.71039   0.44188   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-01-20 Hatching Embryo Trunk Surface Structure
61688 61688 SRR13302966 SRX9731824 SRS7924603 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       NoV△B2: Ago2 IP 3 dpi GSM4988099   source name:zebrafish whole body|zebrafish background:AB|infection:NoV△B2|injection way:microinjection|tissue:zebrafish whole body NoV△B2: Ago2 IP 3 dpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   zebrafish background:AB|infection:NoV△B2|injection way:microinjection|tissue:zebrafish whole body GSM4988099 GSM4988099: NoV△B2: Ago2 IP 3 dpi; Danio rerio; ncRNA Seq GSM4988099   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4988099 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     LY272.fq.gz fastq 2608504950.0 17390033.0 GSM4988099 r1 0:150 1:0 A:741941121;C:669191911;G:747181676;T:450096994;N:93248 150 0     741941121 669191911 747181676 450096994 93248 SRX9731824 SRS7924603 SRA1151114 GEO Fudan University 1 0.13133   0.03425   0.96802   0.60095   150   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-12-24 Undetermined Larval Trunk Surface Structure
61689 61689 SRR12951276 SRX9404383 SRS7622158 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       SINV: zebrafish 3 dpi GSM4873784   source name:zebrafish whole body|tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB SINV: zebrafish 3 dpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB GSM4873784 GSM4873784: SINV: zebrafish 3 dpi; Danio rerio; ncRNA Seq GSM4873784   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873784 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP290217     4_LY215.fq.gz fastq 1328044600.0 26560892.0 GSM4873784 r1 0:50 1:0 A:383401484;C:303337306;G:339848340;T:301397824;N:59646 50 0     383401484 303337306 339848340 301397824 59646 SRX9404383 SRS7622158 SRA1151114 GEO Fudan University 1 0.83242   0.11559   0.93634   0.53516   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
61690 61690 SRR12951275 SRX9404382 SRS7622159 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       VSV: zebrafish 24 hpi GSM4873783   source name:zebrafish whole body|tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB VSV: zebrafish 24 hpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB GSM4873783 GSM4873783: VSV: zebrafish 24 hpi; Danio rerio; ncRNA Seq GSM4873783   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873783 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     3_LY157.fq.gz fastq 706147852.0 29418915.0 GSM4873783 r1 0:24.00 1:0 A:151681768;C:131117267;G:189016204;T:234316361;N:16252 24 0     151681768 131117267 189016204 234316361 16252 SRX9404382 SRS7622159 SRA1151114 GEO Fudan University 1 0.92973   0.12628   0.90664   0.45104   23   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
61691 61691 SRR12951274 SRX9404381 SRS7622157 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       NoV△B2: zebrafish 24 hpi GSM4873782   source name:zebrafish whole body|tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB NoV△B2: zebrafish 24 hpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB GSM4873782 GSM4873782: NoV△B2: zebrafish 24 hpi; Danio rerio; ncRNA Seq GSM4873782   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873782 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     2_LY156.fq.gz fastq 748544818.0 30779865.0 GSM4873782 r1 0:24.32 1:0 A:166631198;C:138321792;G:208615021;T:234953337;N:23470 24 0     166631198 138321792 208615021 234953337 23470 SRX9404381 SRS7622157 SRA1151114 GEO Fudan University 1 0.94115   0.12368   0.91076   0.48684   23   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
61692 61692 SRR12951273 SRX9404380 SRS7622156 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       NoV: zebrafish 24 hpi GSM4873781   source name:zebrafish whole body|tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB NoV: zebrafish 24 hpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB GSM4873781 GSM4873781: NoV: zebrafish 24 hpi; Danio rerio; ncRNA Seq GSM4873781   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873781 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     1_LY155.fq.gz fastq 594676353.0 25019145.0 GSM4873781 r1 0:23.77 1:0 A:129139705;C:108465388;G:162500636;T:194556532;N:14092 23 0     129139705 108465388 162500636 194556532 14092 SRX9404380 SRS7622156 SRA1151114 GEO Fudan University 1 0.93471   0.10892   0.90814   0.48797   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
63515 63515 SRR13865268 SRX10245815 SRS8386823 SRP309488 PRJNA707026 Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [RNA seq] GSE168359 Transcriptome Analysis Vertebrate embryos achieve developmental competency during zygotic genome activation ZGA by establishing chromatin states that silence yet poise developmental genes for subsequent lineage specific activation. Here we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with 'Placeholder' nucleosomes bearing H2A.Z H3K4me1 and H3K27ac and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 PRC1 and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA H2Aub1 enables Aebp2 containing PRC2 recruitment and H3K27me3 deposition. Notably preventing H2Aub1 via Rnf2 inhibition eliminates recruitment of Aebp2 PRC2 and H3K27me3 and elicits transcriptional upregulation of certain developmental genes during ZGA. However upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos. Overall design: RNA seq in early Zebrafish embryos. parent bioproject:PRJNA707023 pubmed:34982026   4hpf DMSO RNAseq rep3 GSM5136700   source name:WT Tubingen|strain:Tubingen|genotype:WT|developmental stage:4hpf|tissue:Whole body embryo|treatment:DMSO 4hpf DMSO RNAseq rep3 RNA seq fastq files were aligned to Zv10 using STAR v2.5.4a with the following settings: runMode alignReads twopassMode Basic alignIntronMax 50000 outSAMtype BAM SortedByCoordinate outWigType bedGraph outWigStrand Unstranded. BAM files were subsequently indexed using Samtools v1.8. FeatureCounts v1.5.1 was utilized to collect count data for zv10 Ensemble v90 genes via the following command: T 16 s 2 –largestOverlap. Count data for all replicates across experimental conditions were combined into a single count matrix in R. The count matrix was subsequently used to identify differentially expressed genes with the R package DESeq2 v1.18. For generation of bigwig files Bam files for a given condition were merged sorted and indexed with samtools. Subsequently deepTools bamCoverage v2.5.4 was used with the normlizeUsingRPKM option to produce bigwig files. Genome build: zv10 Supplementary files format and content: 4hpf PRT4165 vs DMSO RNaseq counts.txt: The count matrix contains data regarding the number of counts each experimental replicate has across zv10 Ensembl v90 transcripts. Supplementary files format and content: *.bw: The bigWig files contain RNA seq signal normalized by RPKM. WT Tubingen Embryo media was supplemented with 150 μM PRT4165 or DMSO from when the embryos were at the 1 cell stage until the embryos were harvested. Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. Standard zebrafish growth conditions. strain:Tubingen|genotype:WT|developmental stage:4hpf|tissue:Whole body embryo|treatment:DMSO GSM5136700 GSM5136700: 4hpf DMSO RNAseq rep3; Danio rerio; RNA Seq GSM5136700   1 Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. GEO Accession:GSM5136700 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP309488     15111X6_180525_D00550_0507_ACCL6GANXX_3.txt fastq 2491105950.0 49822119.0 GSM5136700 r1 0:50 1:0 A:605732242;C:611812186;G:577160273;T:696240551;N:160698 50 0     605732242 611812186 577160273 696240551 160698 SRX10245815 SRS8386823 SRA1203419 GEO Cairns Lab, Oncological Sciences, University of Utah 1 0.96327   0.04471   0.74095   0.48987   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2021-03-05 Blastula Embryo Trunk Surface Structure
63516 63516 SRR13865267 SRX10245814 SRS8386822 SRP309488 PRJNA707026 Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [RNA seq] GSE168359 Transcriptome Analysis Vertebrate embryos achieve developmental competency during zygotic genome activation ZGA by establishing chromatin states that silence yet poise developmental genes for subsequent lineage specific activation. Here we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with 'Placeholder' nucleosomes bearing H2A.Z H3K4me1 and H3K27ac and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 PRC1 and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA H2Aub1 enables Aebp2 containing PRC2 recruitment and H3K27me3 deposition. Notably preventing H2Aub1 via Rnf2 inhibition eliminates recruitment of Aebp2 PRC2 and H3K27me3 and elicits transcriptional upregulation of certain developmental genes during ZGA. However upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos. Overall design: RNA seq in early Zebrafish embryos. parent bioproject:PRJNA707023 pubmed:34982026   4hpf DMSO RNAseq rep2 GSM5136699   source name:WT Tubingen|strain:Tubingen|genotype:WT|developmental stage:4hpf|tissue:Whole body embryo|treatment:DMSO 4hpf DMSO RNAseq rep2 RNA seq fastq files were aligned to Zv10 using STAR v2.5.4a with the following settings: runMode alignReads twopassMode Basic alignIntronMax 50000 outSAMtype BAM SortedByCoordinate outWigType bedGraph outWigStrand Unstranded. BAM files were subsequently indexed using Samtools v1.8. FeatureCounts v1.5.1 was utilized to collect count data for zv10 Ensemble v90 genes via the following command: T 16 s 2 –largestOverlap. Count data for all replicates across experimental conditions were combined into a single count matrix in R. The count matrix was subsequently used to identify differentially expressed genes with the R package DESeq2 v1.18. For generation of bigwig files Bam files for a given condition were merged sorted and indexed with samtools. Subsequently deepTools bamCoverage v2.5.4 was used with the normlizeUsingRPKM option to produce bigwig files. Genome build: zv10 Supplementary files format and content: 4hpf PRT4165 vs DMSO RNaseq counts.txt: The count matrix contains data regarding the number of counts each experimental replicate has across zv10 Ensembl v90 transcripts. Supplementary files format and content: *.bw: The bigWig files contain RNA seq signal normalized by RPKM. WT Tubingen Embryo media was supplemented with 150 μM PRT4165 or DMSO from when the embryos were at the 1 cell stage until the embryos were harvested. Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. Standard zebrafish growth conditions. strain:Tubingen|genotype:WT|developmental stage:4hpf|tissue:Whole body embryo|treatment:DMSO GSM5136699 GSM5136699: 4hpf DMSO RNAseq rep2; Danio rerio; RNA Seq GSM5136699   1 Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. GEO Accession:GSM5136699 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP309488     15111X5_180525_D00550_0507_ACCL6GANXX_3.txt fastq 2557172750.0 51143455.0 GSM5136699 r1 0:50 1:0 A:610458854;C:634365750;G:598885406;T:713297673;N:165067 50 0     610458854 634365750 598885406 713297673 165067 SRX10245814 SRS8386822 SRA1203419 GEO Cairns Lab, Oncological Sciences, University of Utah 1 0.96345   0.04194   0.73848   0.48377   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2021-03-05 Blastula Embryo Trunk Surface Structure
63517 63517 SRR13865266 SRX10245813 SRS8386819 SRP309488 PRJNA707026 Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [RNA seq] GSE168359 Transcriptome Analysis Vertebrate embryos achieve developmental competency during zygotic genome activation ZGA by establishing chromatin states that silence yet poise developmental genes for subsequent lineage specific activation. Here we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with 'Placeholder' nucleosomes bearing H2A.Z H3K4me1 and H3K27ac and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 PRC1 and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA H2Aub1 enables Aebp2 containing PRC2 recruitment and H3K27me3 deposition. Notably preventing H2Aub1 via Rnf2 inhibition eliminates recruitment of Aebp2 PRC2 and H3K27me3 and elicits transcriptional upregulation of certain developmental genes during ZGA. However upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos. Overall design: RNA seq in early Zebrafish embryos. parent bioproject:PRJNA707023 pubmed:34982026   4hpf DMSO RNAseq rep1 GSM5136698   source name:WT Tubingen|strain:Tubingen|genotype:WT|developmental stage:4hpf|tissue:Whole body embryo|treatment:DMSO 4hpf DMSO RNAseq rep1 RNA seq fastq files were aligned to Zv10 using STAR v2.5.4a with the following settings: runMode alignReads twopassMode Basic alignIntronMax 50000 outSAMtype BAM SortedByCoordinate outWigType bedGraph outWigStrand Unstranded. BAM files were subsequently indexed using Samtools v1.8. FeatureCounts v1.5.1 was utilized to collect count data for zv10 Ensemble v90 genes via the following command: T 16 s 2 –largestOverlap. Count data for all replicates across experimental conditions were combined into a single count matrix in R. The count matrix was subsequently used to identify differentially expressed genes with the R package DESeq2 v1.18. For generation of bigwig files Bam files for a given condition were merged sorted and indexed with samtools. Subsequently deepTools bamCoverage v2.5.4 was used with the normlizeUsingRPKM option to produce bigwig files. Genome build: zv10 Supplementary files format and content: 4hpf PRT4165 vs DMSO RNaseq counts.txt: The count matrix contains data regarding the number of counts each experimental replicate has across zv10 Ensembl v90 transcripts. Supplementary files format and content: *.bw: The bigWig files contain RNA seq signal normalized by RPKM. WT Tubingen Embryo media was supplemented with 150 μM PRT4165 or DMSO from when the embryos were at the 1 cell stage until the embryos were harvested. Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. Standard zebrafish growth conditions. strain:Tubingen|genotype:WT|developmental stage:4hpf|tissue:Whole body embryo|treatment:DMSO GSM5136698 GSM5136698: 4hpf DMSO RNAseq rep1; Danio rerio; RNA Seq GSM5136698   1 Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. GEO Accession:GSM5136698 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP309488     15111X4_180525_D00550_0507_ACCL6GANXX_3.txt fastq 1585746950.0 31714939.0 GSM5136698 r1 0:50 1:0 A:378866016;C:394366730;G:370347444;T:442063810;N:102950 50 0     378866016 394366730 370347444 442063810 102950 SRX10245813 SRS8386819 SRA1203419 GEO Cairns Lab, Oncological Sciences, University of Utah 1 0.96407   0.0405   0.73914   0.48652   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2021-03-05 Blastula Embryo Trunk Surface Structure

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