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
32,DRR408242,DRX393848,DRS407006,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 3,zebrafish adult gut replicate 3,SAMD00529462,,sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529462,DRX393848,AR019 gut 6  adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529462,,,,3546347364.0,28145614.0,DRR408242,0:126 1:0,A:919466631;C:829424335;G:818581155;T:978810217;N:65026,126,0,,,919466631,829424335,818581155,978810217,65026,DRX393848,DRS407006,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
33,DRR408241,DRX393847,DRS407005,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 2,zebrafish adult gut replicate 2,SAMD00529461,,sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529461,DRX393847,AR006 gut 4  adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529461,,,,3671973648.0,29142648.0,DRR408241,0:126 1:0,A:942167543;C:859431290;G:852661772;T:1017643011;N:70032,126,0,,,942167543,859431290,852661772,1017643011,70032,DRX393847,DRS407005,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
34,DRR408240,DRX393846,DRS407004,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB adult gut replicate 1,zebrafish adult gut replicate 1,SAMD00529460,,sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529460,DRX393846,AR004 gut 2  adult,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529460,,,,3480523704.0,27623204.0,DRR408240,0:126 1:0,A:898051986;C:827557593;G:816541244;T:938307607;N:65274,126,0,,,898051986,827557593,816541244,938307607,65274,DRX393846,DRS407004,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
35,DRR408239,DRX393845,DRS407003,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 3,zebrafish larval gut replicate 3,SAMD00529459,,sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529459,DRX393845,AR012 gut 5  5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529459,,,,3463982046.0,27491921.0,DRR408239,0:126 1:0,A:842552557;C:849757648;G:837664725;T:933942026;N:65090,126,0,,,842552557,849757648,837664725,933942026,65090,DRX393845,DRS407003,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
36,DRR408238,DRX393844,DRS407002,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 2,zebrafish larval gut replicate 2,SAMD00529458,,sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529458,DRX393844,AR005 gut 3  5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529458,,,,3782320416.0,30018416.0,DRR408238,0:126 1:0,A:930337206;C:920645770;G:906559955;T:1024704277;N:73208,126,0,,,930337206,920645770,906559955,1024704277,73208,DRX393844,DRS407002,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
37,DRR408237,DRX393843,DRS407001,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 1,zebrafish larval gut replicate 1,SAMD00529457,,sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529457,DRX393843,AR002 gut 1  5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529457,,,,3606885828.0,28626078.0,DRR408237,0:126 1:0,A:879148446;C:885673723;G:870330963;T:971663212;N:69484,126,0,,,879148446,885673723,870330963,971663212,69484,DRX393843,DRS407001,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
172,DRR075398,DRX069312,DRS075493,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 gut of control fish 7dpf,Control gut,SAMD00065412,,sample name:2 control gut 150701 Hiseq3A l3 018|tissue type:Gut,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065412,DRX069312,Control gut,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 SAMD00065412,,,,1008093492.0,28002597.0,DRR075398,0:36,A:230431417;C:251640901;G:244174255;T:281811580;N:35339,36,,,,230431417,251640901,244174255,281811580,35339,DRX069312,DRS075493,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",1,0.9173,,0.07181,,0.72017,,0.45193,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Gut,Digestive System
24918,SRR25594442,SRX21322829,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,Z 2 1.fq,Z 2 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,Z-2_2.fq.gz Z-2_1.fq.gz,fastq fastq,5621492400.0,18738308.0,Z 2 1.fq.gz,0:150 1:150,A:1483421677;C:1306378425;G:1338052121;T:1493618330;N:21847,150,150,,,1483421677,1306378425,1338052121,1493618330,21847,SRX21322829,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94389,0.93819,0.03702,0.03621,0.71758,0.72423,0.43774,0.4558,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24919,SRR25594443,SRX21322828,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,Z 1 1.fq,Z 1 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,Z-1_2.fq.gz Z-1_1.fq.gz,fastq fastq,6301274700.0,21004249.0,Z 1 1.fq.gz,0:150 1:150,A:1671253253;C:1458678359;G:1491311308;T:1680006330;N:25450,150,150,,,1671253253,1458678359,1491311308,1680006330,25450,SRX21322828,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94339,0.93817,0.03831,0.03813,0.71752,0.72293,0.42611,0.43548,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24920,SRR25594444,SRX21322827,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,K 3 1.fq,K 3 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,K-3_2.fq.gz K-3_1.fq.gz,fastq fastq,5519682000.0,18398940.0,K 3 1.fq.gz,0:150 1:150,A:1469946965;C:1270791684;G:1304075220;T:1474846842;N:21289,150,150,,,1469946965,1270791684,1304075220,1474846842,21289,SRX21322827,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94356,0.93561,0.03986,0.03923,0.71877,0.72697,0.44771,0.44936,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24921,SRR25594445,SRX21322826,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,K 2 1.fq,K 2 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,K-2_1.fq.gz K-2_2.fq.gz,fastq fastq,5808261300.0,19360871.0,K 2 1.fq.gz,0:150 1:150,A:1538012312;C:1343217111;G:1375887577;T:1551118640;N:25660,150,150,,,1538012312,1343217111,1375887577,1551118640,25660,SRX21322826,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94469,0.94137,0.03929,0.03857,0.7175,0.71946,0.44395,0.44354,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24922,SRR25594446,SRX21322825,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,ZP 3 1.fq,ZP 3 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,ZP-3_1.fq.gz ZP-3_2.fq.gz,fastq fastq,5397938100.0,17993127.0,ZP 3 1.fq.gz,0:150 1:150,A:1438191584;C:1244532731;G:1271700792;T:1443491138;N:21855,150,150,,,1438191584,1244532731,1271700792,1443491138,21855,SRX21322825,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94839,0.94406,0.04345,0.04279,0.71719,0.72362,0.42772,0.4311,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24923,SRR25594447,SRX21322824,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,ZP 2 1.fq,ZP 2 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,ZP-2_1.fq.gz ZP-2_2.fq.gz,fastq fastq,6062424900.0,20208083.0,ZP 2 1.fq.gz,0:150 1:150,A:1612595576;C:1398589726;G:1427536119;T:1623678727;N:24752,150,150,,,1612595576,1398589726,1427536119,1623678727,24752,SRX21322824,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.95013,0.94657,0.04364,0.04342,0.71565,0.71908,0.44652,0.44832,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24924,SRR25594448,SRX21322823,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,ZP 1 1.fq,ZP 1 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,ZP-1_2.fq.gz ZP-1_1.fq.gz,fastq fastq,6487607100.0,21625357.0,ZP 1 1.fq.gz,0:150 1:150,A:1728514584;C:1494175744;G:1521726756;T:1743164500;N:25516,150,150,,,1728514584,1494175744,1521726756,1743164500,25516,SRX21322823,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94867,0.94432,0.04535,0.0449,0.71926,0.72348,0.43747,0.44661,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24925,SRR25594449,SRX21322822,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,Z 3 1.fq,Z 3 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,Z-3_1.fq.gz Z-3_2.fq.gz,fastq fastq,8111204700.0,27037349.0,Z 3 1.fq.gz,0:150 1:150,A:2143712842;C:1879826122;G:1918517283;T:2169119328;N:29125,150,150,,,2143712842,1879826122,1918517283,2169119328,29125,SRX21322822,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94485,0.94083,0.03886,0.03798,0.71362,0.71768,0.44066,0.44713,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24926,SRR25594450,SRX21322821,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,K 1 1.fq,K 1 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,K-1_1.fq.gz K-1_2.fq.gz,fastq fastq,7164142200.0,23880474.0,K 1 1.fq.gz,0:150 1:150,A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789,150,150,,,1896647470,1661542391,1700422400,1905500150,29789,SRX21322821,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94635,0.94209,0.03738,0.03664,0.71961,0.72571,0.45014,0.44857,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
29041,SRR26990794,SRX22683825,SRS19677539,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut3,GSM7924158,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924158,GSM7924158: WT gut3; Danio rerio; RNA Seq,GSM7924158 r1,GSM7924158,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz,fastq fastq,6066709786.0,20088443.0,GSM7924158 r1,0:151 1:151,A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156,151,151,,,1673762656,1360901090,1385125931,1646863953,56156,SRX22683825,SRS19677539,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.92515,0.9297,0.0691,0.0659,0.75041,0.75022,0.53007,0.53064,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29042,SRR26990795,SRX22683824,SRS19677538,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut2,GSM7924157,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924157,GSM7924157: WT gut2; Danio rerio; RNA Seq,GSM7924157 r1,GSM7924157,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz,fastq fastq,5406867570.0,17903535.0,GSM7924157 r1,0:151 1:151,A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612,151,151,,,1464846243,1237183908,1259215309,1445572498,49612,SRX22683824,SRS19677538,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93795,0.94322,0.05952,0.05592,0.75933,0.75887,0.54179,0.53451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29043,SRR26990796,SRX22683823,SRS19677537,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut1,GSM7924156,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924156,GSM7924156: WT gut1; Danio rerio; RNA Seq,GSM7924156 r1,GSM7924156,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz,fastq fastq,5162192908.0,17093354.0,GSM7924156 r1,0:151 1:151,A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343,151,151,,,1404682153,1175657030,1196829496,1384975886,48343,SRX22683823,SRS19677537,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93119,0.93585,0.06122,0.05809,0.74757,0.74757,0.54124,0.54417,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29044,SRR26990797,SRX22683822,SRS19677536,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut3,GSM7924155,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924155,GSM7924155: itgavKO gut3; Danio rerio; RNA Seq,GSM7924155 r1,GSM7924155,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz,fastq fastq,4146743578.0,13730939.0,GSM7924155 r1,0:151 1:151,A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387,151,151,,,1130002132,943522869,958031732,1115146458,40387,SRX22683822,SRS19677536,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93764,0.94144,0.05938,0.05594,0.7553,0.75485,0.55535,0.55018,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29045,SRR26990798,SRX22683821,SRS19677535,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut2,GSM7924154,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924154,GSM7924154: itgavKO gut2; Danio rerio; RNA Seq,GSM7924154 r1,GSM7924154,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz,fastq fastq,4225756140.0,13992570.0,GSM7924154 r1,0:151 1:151,A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530,151,151,,,1133211420,974497998,995876972,1122129220,40530,SRX22683821,SRS19677535,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.95341,0.95884,0.05109,0.04883,0.77542,0.77368,0.51301,0.50704,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29046,SRR26990799,SRX22683820,SRS19677534,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itagvKO gut1,GSM7924153,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itagvKO gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924153,GSM7924153: itagvKO gut1; Danio rerio; RNA Seq,GSM7924153 r1,GSM7924153,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz,fastq fastq,5954117844.0,19715622.0,GSM7924153 r1,0:151 1:151,A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859,151,151,,,1600496071,1372939932,1393534700,1587094282,52859,SRX22683820,SRS19677534,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.94807,0.95298,0.05682,0.05385,0.74004,0.73925,0.54423,0.54484,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29575,SRR27387418,SRX23063709,SRS20023731,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 6,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate6|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 6,T8 6,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A54_1.fastq.gz A54_2.fastq.gz,fastq fastq,8459790000.0,28199300.0,A54 1.fastq.gz,0:150 1:150,A:2287135948;C:1957145280;G:1959338891;T:2256075943;N:93938,150,150,,,2287135948,1957145280,1959338891,2256075943,93938,SRX23063709,SRS20023731,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92583,0.92422,0.06345,0.06263,0.75718,0.75757,0.52145,0.5361,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29576,SRR27387419,SRX23063708,SRS20023730,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 5,T8 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A53_1.fastq.gz A53_2.fastq.gz,fastq fastq,8302022700.0,27673409.0,A53 1.fastq.gz,0:150 1:150,A:2241277601;C:1925048164;G:1920142999;T:2215462687;N:91249,150,150,,,2241277601,1925048164,1920142999,2215462687,91249,SRX23063708,SRS20023730,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92711,0.92566,0.06314,0.06353,0.75221,0.75219,0.541,0.53579,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29577,SRR27387420,SRX23063707,SRS20023729,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 4,T8 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A49_1.fastq.gz A49_2.fastq.gz,fastq fastq,6939976800.0,23133256.0,A49 1.fastq.gz,0:150 1:150,A:1895013575;C:1589528661;G:1585890890;T:1869466351;N:77323,150,150,,,1895013575,1589528661,1585890890,1869466351,77323,SRX23063707,SRS20023729,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92632,0.92542,0.06323,0.06265,0.75588,0.75722,0.55002,0.55324,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29578,SRR27387421,SRX23063706,SRS20023728,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 3,T8 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A44_1.fastq.gz A44_2.fastq.gz,fastq fastq,9116379900.0,30387933.0,A44 1.fastq.gz,0:150 1:150,A:2462347514;C:2113718621;G:2112401730;T:2427812186;N:99849,150,150,,,2462347514,2113718621,2112401730,2427812186,99849,SRX23063706,SRS20023728,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93154,0.92882,0.06321,0.06277,0.75499,0.75519,0.54224,0.542,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29579,SRR27387422,SRX23063705,SRS20023727,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 2,T8 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A43_1.fastq.gz A43_2.fastq.gz,fastq fastq,7681997100.0,25606657.0,A43 1.fastq.gz,0:150 1:150,A:2098281007;C:1758609887;G:1757658923;T:2067364339;N:82944,150,150,,,2098281007,1758609887,1757658923,2067364339,82944,SRX23063705,SRS20023727,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92257,0.92131,0.07154,0.07125,0.74769,0.74712,0.52352,0.51843,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29580,SRR27387423,SRX23063704,SRS20023726,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 1,T8 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A29_1.fastq.gz A29_2.fastq.gz,fastq fastq,8869294500.0,29564315.0,A29 1.fastq.gz,0:150 1:150,A:2411657291;C:2043119196;G:2038118093;T:2376336869;N:63051,150,150,,,2411657291,2043119196,2038118093,2376336869,63051,SRX23063704,SRS20023726,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.9293,0.93157,0.06846,0.06859,0.75138,0.75209,0.54348,0.54178,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29582,SRR27387425,SRX23063702,SRS20023724,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 5,T7 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A51_1.fastq.gz A51_2.fastq.gz,fastq fastq,8229865500.0,27432885.0,A51 1.fastq.gz,0:150 1:150,A:2239224965;C:1891494000;G:1890511233;T:2208544358;N:90944,150,150,,,2239224965,1891494000,1890511233,2208544358,90944,SRX23063702,SRS20023724,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.9282,0.92676,0.06786,0.06815,0.74566,0.74673,0.54961,0.55067,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29583,SRR27387426,SRX23063701,SRS20023723,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 4,T7 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A50_1.fastq.gz A50_2.fastq.gz,fastq fastq,8549274300.0,28497581.0,A50 1.fastq.gz,0:150 1:150,A:2321938070;C:1971518879;G:1967040023;T:2288683614;N:93714,150,150,,,2321938070,1971518879,1967040023,2288683614,93714,SRX23063701,SRS20023723,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93231,0.93126,0.06361,0.06304,0.7527,0.75211,0.48289,0.48336,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29584,SRR27387427,SRX23063700,SRS20023722,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 3,T7 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A48_1.fastq.gz A48_2.fastq.gz,fastq fastq,8065026000.0,26883420.0,A48 1.fastq.gz,0:150 1:150,A:2177870889;C:1870003683;G:1870725132;T:2146337507;N:88789,150,150,,,2177870889,1870003683,1870725132,2146337507,88789,SRX23063700,SRS20023722,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92891,0.92753,0.05842,0.05778,0.71991,0.72009,0.51653,0.51675,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29585,SRR27387428,SRX23063699,SRS20023721,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 2,T7 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A42_1.fastq.gz A42_2.fastq.gz,fastq fastq,8391356700.0,27971189.0,A42 1.fastq.gz,0:150 1:150,A:2247673277;C:1962692430;G:1966871884;T:2214026582;N:92527,150,150,,,2247673277,1962692430,1966871884,2214026582,92527,SRX23063699,SRS20023721,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93153,0.93045,0.05902,0.05934,0.75424,0.75546,0.548,0.54354,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29586,SRR27387429,SRX23063698,SRS20023720,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 1,T7 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A31_1.fastq.gz A31_2.fastq.gz,fastq fastq,8236557000.0,27455190.0,A31 1.fastq.gz,0:150 1:150,A:2204148101;C:1929010419;G:1925723147;T:2177582914;N:92419,150,150,,,2204148101,1929010419,1925723147,2177582914,92419,SRX23063698,SRS20023720,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93739,0.93581,0.06216,0.06176,0.75057,0.75049,0.54176,0.53414,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29587,SRR27387430,SRX23063697,SRS20023719,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 6,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate6|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 6,T6 6,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A56_1.fastq.gz A56_2.fastq.gz,fastq fastq,6435464400.0,21451548.0,A56 1.fastq.gz,0:150 1:150,A:1748400934;C:1486171533;G:1481023797;T:1719795546;N:72590,150,150,,,1748400934,1486171533,1481023797,1719795546,72590,SRX23063697,SRS20023719,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92722,0.92559,0.0729,0.07288,0.74288,0.74343,0.53587,0.52589,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29588,SRR27387431,SRX23063696,SRS20023718,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 5,T6 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A40_1.fastq.gz A40_2.fastq.gz,fastq fastq,8749914000.0,29166380.0,A40 1.fastq.gz,0:150 1:150,A:2338416402;C:2051360445;G:2055480569;T:2304561447;N:95137,150,150,,,2338416402,2051360445,2055480569,2304561447,95137,SRX23063696,SRS20023718,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.94523,0.9504,0.03896,0.03887,0.80661,0.80728,0.46402,0.45996,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29589,SRR27387432,SRX23063695,SRS20023717,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 4,T6 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A39_1.fastq.gz A39_2.fastq.gz,fastq fastq,8140938300.0,27136461.0,A39 1.fastq.gz,0:150 1:150,A:2198617601;C:1888830697;G:1887283102;T:2166117857;N:89043,150,150,,,2198617601,1888830697,1887283102,2166117857,89043,SRX23063695,SRS20023717,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92636,0.92532,0.05883,0.0588,0.71689,0.71593,0.52397,0.5214,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29590,SRR27387433,SRX23063694,SRS20023716,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 3,T6 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A35_1.fastq.gz A35_2.fastq.gz,fastq fastq,6912319200.0,23041064.0,A35 1.fastq.gz,0:150 1:150,A:1895216825;C:1576630157;G:1574441195;T:1865953455;N:77568,150,150,,,1895216825,1576630157,1574441195,1865953455,77568,SRX23063694,SRS20023716,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92983,0.92816,0.072,0.07173,0.76601,0.76615,0.55997,0.55562,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29591,SRR27387434,SRX23063693,SRS20023715,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 2,T6 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A34_1.fastq.gz A34_2.fastq.gz,fastq fastq,7279802100.0,24266007.0,A34 1.fastq.gz,0:150 1:150,A:1989158951;C:1663891494;G:1668311413;T:1958359476;N:80766,150,150,,,1989158951,1663891494,1668311413,1958359476,80766,SRX23063693,SRS20023715,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92923,0.92655,0.06821,0.068,0.74042,0.74128,0.54366,0.54276,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29593,SRR27387436,SRX23063691,SRS20023713,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 1,T6 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A30_1.fastq.gz A30_2.fastq.gz,fastq fastq,7219947600.0,24066492.0,A30 1.fastq.gz,0:150 1:150,A:1901354175;C:1717600917;G:1716606554;T:1884305293;N:80661,150,150,,,1901354175,1717600917,1716606554,1884305293,80661,SRX23063691,SRS20023713,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93375,0.93214,0.05513,0.05567,0.74759,0.74698,0.5475,0.54855,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29594,SRR27387437,SRX23063690,SRS20023712,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 6,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate6|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 6,T5 6,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A46_1.fastq.gz A46_2.fastq.gz,fastq fastq,8509361100.0,28364537.0,A46 1.fastq.gz,0:150 1:150,A:2341600956;C:1932495972;G:1930461855;T:2304710926;N:91391,150,150,,,2341600956,1932495972,1930461855,2304710926,91391,SRX23063690,SRS20023712,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92542,0.92408,0.07033,0.06986,0.77234,0.77199,0.55246,0.55942,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29595,SRR27387438,SRX23063689,SRS20023711,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 5,T5 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A45_1.fastq.gz A45_2.fastq.gz,fastq fastq,7856294100.0,26187647.0,A45 1.fastq.gz,0:150 1:150,A:2129077180;C:1813666476;G:1813868805;T:2099595491;N:86148,150,150,,,2129077180,1813666476,1813868805,2099595491,86148,SRX23063689,SRS20023711,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93087,0.92866,0.06398,0.06358,0.75481,0.75597,0.55424,0.55289,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29596,SRR27387439,SRX23063688,SRS20023710,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 4,T5 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A38_1.fastq.gz A38_2.fastq.gz,fastq fastq,8039208600.0,26797362.0,A38 1.fastq.gz,0:150 1:150,A:2201215819;C:1836215616;G:1833348507;T:2168337651;N:91007,150,150,,,2201215819,1836215616,1833348507,2168337651,91007,SRX23063688,SRS20023710,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.9219,0.91957,0.0702,0.06947,0.76343,0.76493,0.55355,0.54863,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29597,SRR27387440,SRX23063687,SRS20023709,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 3,T5 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A37_1.fastq.gz A37_2.fastq.gz,fastq fastq,8253642600.0,27512142.0,A37 1.fastq.gz,0:150 1:150,A:2254958000;C:1889478281;G:1886099650;T:2223014303;N:92366,150,150,,,2254958000,1889478281,1886099650,2223014303,92366,SRX23063687,SRS20023709,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92632,0.92477,0.06268,0.06279,0.76719,0.76682,0.53773,0.53566,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29598,SRR27387441,SRX23063686,SRS20023708,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 2,T5 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A33_1.fastq.gz A33_2.fastq.gz,fastq fastq,8276959500.0,27589865.0,A33 1.fastq.gz,0:150 1:150,A:2244800716;C:1909951370;G:1909130637;T:2212988991;N:87786,150,150,,,2244800716,1909951370,1909130637,2212988991,87786,SRX23063686,SRS20023708,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93248,0.93089,0.06402,0.06475,0.701,0.7012,0.53585,0.53722,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29599,SRR27387442,SRX23063685,SRS20023707,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 1,T5 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A32_1.fastq.gz A32_2.fastq.gz,fastq fastq,7955418900.0,26518063.0,A32 1.fastq.gz,0:150 1:150,A:2236485440;C:1768380410;G:1765867470;T:2184596828;N:88752,150,150,,,2236485440,1768380410,1765867470,2184596828,88752,SRX23063685,SRS20023707,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92662,0.92301,0.071,0.07061,0.75207,0.75158,0.53095,0.54507,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
32923,SRR29498567,SRX25008885,SRS21709104,SRP515416,PRJNA1127032,Zebrafish Tissue Mid Range RNA Sequencing,PRJNA1127032,Other,This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.,,,,,F2g,,strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F2g|BioSampleModel:Model organism or animal,,,,,,,,,midRNA seq Danio rerio,10,10,Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP515416,,,F2g_R2.fq.gz F2g_R1.fq.gz,fastq fastq,9101949000.0,30339830.0,F2g R1.fq.gz,0:150 1:150,A:2052853923;C:2394247721;G:2773304460;T:1881440199;N:102697,150,150,,,2052853923,2394247721,2773304460,1881440199,102697,SRX25008885,SRS21709104,SRA1905460,Eotvos Lorand University|Genetics,Eotvos Lorand University,2,0.65449,0.37434,0.04313,0.12258,0.99519,0.99527,0.61425,0.56139,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Hungary,2024-06-22,Adult,Adult,Gut,Digestive System
32924,SRR29498568,SRX25008884,SRS21709103,SRP515416,PRJNA1127032,Zebrafish Tissue Mid Range RNA Sequencing,PRJNA1127032,Other,This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.,,,,,F1g,,strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F1g|BioSampleModel:Model organism or animal,,,,,,,,,midRNA seq Danio rerio,09,09,Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP515416,,,F1g_R1.fq.gz F1g_R2.fq.gz,fastq fastq,8132653500.0,27108845.0,F1g R1.fq.gz,0:150 1:150,A:1811779602;C:2095863397;G:2529881799;T:1695036688;N:92014,150,150,,,1811779602,2095863397,2529881799,1695036688,92014,SRX25008884,SRS21709103,SRA1905460,Eotvos Lorand University|Genetics,Eotvos Lorand University,2,0.53909,0.24181,0.01966,0.04797,0.99598,0.99624,0.59302,0.62038,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Hungary,2024-06-22,Adult,Adult,Gut,Digestive System
32931,SRR29498575,SRX25008877,SRS21709096,SRP515416,PRJNA1127032,Zebrafish Tissue Mid Range RNA Sequencing,PRJNA1127032,Other,This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.,,,,,M2g,,strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M2g|BioSampleModel:Model organism or animal,,,,,,,,,midRNA seq Danio rerio,12,12,Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP515416,,,M2g_R1.fq.gz M2g_R2.fq.gz,fastq fastq,7106243100.0,23687477.0,M2g R1.fq.gz,0:150 1:150,A:1567154123;C:1866065312;G:2213286944;T:1459656676;N:80045,150,150,,,1567154123,1866065312,2213286944,1459656676,80045,SRX25008877,SRS21709096,SRA1905460,Eotvos Lorand University|Genetics,Eotvos Lorand University,2,0.56476,0.25026,0.02259,0.04481,0.99667,0.99701,0.63277,0.65693,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Hungary,2024-06-22,Adult,Adult,Gut,Digestive System
32932,SRR29498576,SRX25008876,SRS21709095,SRP515416,PRJNA1127032,Zebrafish Tissue Mid Range RNA Sequencing,PRJNA1127032,Other,This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.,,,,,M1g,,strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M1g|BioSampleModel:Model organism or animal,,,,,,,,,midRNA seq Danio rerio,11,11,Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP515416,,,M1g_R2.fq.gz M1g_R1.fq.gz,fastq fastq,7351182000.0,24503940.0,M1g R1.fq.gz,0:150 1:150,A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321,150,150,,,1623685246,1858847576,2315396486,1553169371,83321,SRX25008876,SRS21709095,SRA1905460,Eotvos Lorand University|Genetics,Eotvos Lorand University,2,0.96004,0.21521,0.16113,0.04578,0.92431,0.99143,0.61867,0.63432,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Hungary,2024-06-22,Adult,Adult,Gut,Digestive System
33351,SRR30125634,SRX25595192,SRS22245033,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 3,GSM8439539,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439539,GSM8439539: SBM1 3; Danio rerio; RNA Seq,GSM8439539 r1,GSM8439539,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-3.R1.fq.gz SBM1-3.R2.fq.gz,fastq fastq,6920938402.0,24030624.0,GSM8439539 r1,0:144.00 1:144.00,A:1848518187;C:1602695225;G:1609135376;T:1860572175;N:17439,144,144,,,1848518187,1602695225,1609135376,1860572175,17439,SRX25595192,SRS22245033,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33352,SRR30125635,SRX25595191,SRS22245032,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 2,GSM8439538,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439538,GSM8439538: SBM1 2; Danio rerio; RNA Seq,GSM8439538 r1,GSM8439538,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-2.R1.fq.gz SBM1-2.R2.fq.gz,fastq fastq,6873386097.0,23812133.0,GSM8439538 r1,0:144.32 1:144.33,A:1794801562;C:1631426136;G:1638460090;T:1808681001;N:17308,144,144,,,1794801562,1631426136,1638460090,1808681001,17308,SRX25595191,SRS22245032,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33353,SRR30125636,SRX25595190,SRS22245031,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 1,GSM8439537,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439537,GSM8439537: SBM1 1; Danio rerio; RNA Seq,GSM8439537 r1,GSM8439537,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-1.R1.fq.gz SBM1-1.R2.fq.gz,fastq fastq,6893638362.0,23881631.0,GSM8439537 r1,0:144.33 1:144.33,A:1801507713;C:1634518350;G:1642455999;T:1815139080;N:17220,144,144,,,1801507713,1634518350,1642455999,1815139080,17220,SRX25595190,SRS22245031,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33354,SRR30125637,SRX25595189,SRS22245030,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 3,GSM8439536,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439536,GSM8439536: FM1 3; Danio rerio; RNA Seq,GSM8439536 r1,GSM8439536,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-3.R1.fq.gz FM1-3.R2.fq.gz,fastq fastq,6926890624.0,24044310.0,GSM8439536 r1,0:144.04 1:144.05,A:1814868011;C:1638590076;G:1645410775;T:1828004537;N:17225,144,144,,,1814868011,1638590076,1645410775,1828004537,17225,SRX25595189,SRS22245030,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33355,SRR30125638,SRX25595188,SRS22245029,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 2,GSM8439535,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439535,GSM8439535: FM1 2; Danio rerio; RNA Seq,GSM8439535 r1,GSM8439535,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-2.R1.fq.gz FM1-2.R2.fq.gz,fastq fastq,6932329149.0,24050700.0,GSM8439535 r1,0:144.12 1:144.12,A:1821635965;C:1634568957;G:1641356498;T:1834750114;N:17615,144,144,,,1821635965,1634568957,1641356498,1834750114,17615,SRX25595188,SRS22245029,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33356,SRR30125639,SRX25595187,SRS22245028,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 1,GSM8439534,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439534,GSM8439534: FM1 1; Danio rerio; RNA Seq,GSM8439534 r1,GSM8439534,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-1.R1.fq.gz FM1-1.R2.fq.gz,fastq fastq,6915521492.0,24044109.0,GSM8439534 r1,0:143.81 1:143.81,A:1851629842;C:1595942468;G:1602547587;T:1865384194;N:17401,143,143,,,1851629842,1595942468,1602547587,1865384194,17401,SRX25595187,SRS22245028,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33357,SRR30125640,SRX25595186,SRS22245027,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 3,GSM8439533,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439533,GSM8439533: D3 4 3; Danio rerio; RNA Seq,GSM8439533 r1,GSM8439533,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-3.R1.fq.gz D3-4-3.R2.fq.gz,fastq fastq,6934859246.0,24095045.0,GSM8439533 r1,0:143.91 1:143.91,A:1815846879;C:1641161510;G:1648091770;T:1829741658;N:17429,143,143,,,1815846879,1641161510,1648091770,1829741658,17429,SRX25595186,SRS22245027,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33358,SRR30125641,SRX25595185,SRS22245026,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 2,GSM8439532,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439532,GSM8439532: D3 4 2; Danio rerio; RNA Seq,GSM8439532 r1,GSM8439532,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-2.R1.fq.gz D3-4-2.R2.fq.gz,fastq fastq,7053487385.0,24519028.0,GSM8439532 r1,0:143.83 1:143.84,A:1888591272;C:1630003556;G:1636509489;T:1898365125;N:17943,143,143,,,1888591272,1630003556,1636509489,1898365125,17943,SRX25595185,SRS22245026,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33359,SRR30125642,SRX25595184,SRS22245025,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 1,GSM8439531,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439531,GSM8439531: D3 4 1; Danio rerio; RNA Seq,GSM8439531 r1,GSM8439531,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz,fastq fastq,6996797279.0,24229469.0,GSM8439531 r1,0:144.38 1:144.39,A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723,144,144,,,1841905352,1647600285,1654313322,1852960597,17723,SRX25595184,SRS22245025,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
34137,SRR31360761,SRX26734629,SRS23224778,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT3,,strain:AB|isolate:WT3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT3.fq,WT3.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT3_R1.fq.gz WT3_R2.fq.gz,fastq fastq,7045875300.0,23486251.0,WT3 R1.fq.gz,0:150 1:150,A:1817741681;C:1708030651;G:1712073267;T:1808003621;N:26080,150,150,,,1817741681,1708030651,1712073267,1808003621,26080,SRX26734629,SRS23224778,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34138,SRR31360762,SRX26734628,SRS23224777,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT2,,strain:AB|isolate:WT2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT2.fq,WT2.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT2_R1.fq.gz WT2_R2.fq.gz,fastq fastq,6888570900.0,22961903.0,WT2 R1.fq.gz,0:150 1:150,A:1774584110;C:1673773734;G:1678866397;T:1761321702;N:24957,150,150,,,1774584110,1673773734,1678866397,1761321702,24957,SRX26734628,SRS23224777,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34139,SRR31360763,SRX26734627,SRS23224776,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT1,,strain:AB|isolate:WT1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT1.fq,WT1.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT1_R1.fq.gz WT1_R2.fq.gz,fastq fastq,6815123400.0,22717078.0,WT1 R1.fq.gz,0:150 1:150,A:1758536338;C:1650339290;G:1657619698;T:1748603714;N:24360,150,150,,,1758536338,1650339290,1657619698,1748603714,24360,SRX26734627,SRS23224776,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34140,SRR31360764,SRX26734626,SRS23224775,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu3,,strain:AB|isolate:mu3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu3.fq,mu3.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu3_R1.fq.gz mu3_R2.fq.gz,fastq fastq,7304650200.0,24348834.0,mu3 R1.fq.gz,0:150 1:150,A:1934717193;C:1720864609;G:1730177787;T:1918863192;N:27419,150,150,,,1934717193,1720864609,1730177787,1918863192,27419,SRX26734626,SRS23224775,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34141,SRR31360765,SRX26734625,SRS23224774,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu2,,strain:AB|isolate:mu2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu2.fq,mu2.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu2_R1.fq.gz mu2_R2.fq.gz,fastq fastq,7168114200.0,23893714.0,mu2 R1.fq.gz,0:150 1:150,A:1896004564;C:1692025000;G:1701080897;T:1878977280;N:26459,150,150,,,1896004564,1692025000,1701080897,1878977280,26459,SRX26734625,SRS23224774,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34142,SRR31360766,SRX26734624,SRS23224773,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu1,,strain:AB|isolate:mu1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu1.fq,mu1.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu1_R1.fq.gz mu1_R2.fq.gz,fastq fastq,7262664600.0,24208882.0,mu1 R1.fq.gz,0:150 1:150,A:1922666653;C:1711620445;G:1720530432;T:1907824480;N:22590,150,150,,,1922666653,1711620445,1720530432,1907824480,22590,SRX26734624,SRS23224773,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34491,SRR31852177,SRX27211969,SRS23661292,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  BG  rep3,GSM8703891,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  BG  rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703891,GSM8703891: Zebrafish  BG  rep3; Danio rerio; RNA Seq,GSM8703891 r1,GSM8703891,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_3_R1.fastq.gz BG_3_R2.fastq.gz,fastq fastq,6899655382.0,22846541.0,GSM8703891 r1,0:151 1:151,A:1811966008;C:1615713130;G:1645022233;T:1826840592;N:113419,151,151,,,1811966008,1615713130,1645022233,1826840592,113419,SRX27211969,SRS23661292,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34492,SRR31852178,SRX27211968,SRS23661291,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  BG  rep2,GSM8703890,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  BG  rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703890,GSM8703890: Zebrafish  BG  rep2; Danio rerio; RNA Seq,GSM8703890 r1,GSM8703890,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_2_R1.fastq.gz BG_2_R2.fastq.gz,fastq fastq,6320533538.0,20928919.0,GSM8703890 r1,0:151 1:151,A:1636247942;C:1501072316;G:1530315619;T:1652793962;N:103699,151,151,,,1636247942,1501072316,1530315619,1652793962,103699,SRX27211968,SRS23661291,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34493,SRR31852179,SRX27211967,SRS23661290,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  BG  rep1,GSM8703889,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  BG  rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703889,GSM8703889: Zebrafish  BG  rep1; Danio rerio; RNA Seq,GSM8703889 r1,GSM8703889,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_1_R1.fastq.gz BG_1_R2.fastq.gz,fastq fastq,6720003132.0,22251666.0,GSM8703889 r1,0:151 1:151,A:1771169227;C:1572565291;G:1597071360;T:1779087569;N:109685,151,151,,,1771169227,1572565291,1597071360,1779087569,109685,SRX27211967,SRS23661290,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34494,SRR31852180,SRX27211966,SRS23661289,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  EIB202  rep3,GSM8703888,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  EIB202  rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703888,GSM8703888: Zebrafish  EIB202  rep3; Danio rerio; RNA Seq,GSM8703888 r1,GSM8703888,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_3_R1.fastq.gz EIB202_3_R2.fastq.gz,fastq fastq,6653244824.0,22030612.0,GSM8703888 r1,0:151 1:151,A:1715767195;C:1587994105;G:1617241387;T:1732132934;N:109203,151,151,,,1715767195,1587994105,1617241387,1732132934,109203,SRX27211966,SRS23661289,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34495,SRR31852181,SRX27211965,SRS23661288,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  EIB202  rep2,GSM8703887,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  EIB202  rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703887,GSM8703887: Zebrafish  EIB202  rep2; Danio rerio; RNA Seq,GSM8703887 r1,GSM8703887,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_2_R1.fastq.gz EIB202_2_R2.fastq.gz,fastq fastq,7203983198.0,23854249.0,GSM8703887 r1,0:151 1:151,A:1847641462;C:1731806146;G:1763208826;T:1861209998;N:116766,151,151,,,1847641462,1731806146,1763208826,1861209998,116766,SRX27211965,SRS23661288,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34496,SRR31852182,SRX27211964,SRS23661287,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  EIB202  rep1,GSM8703886,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  EIB202  rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703886,GSM8703886: Zebrafish  EIB202  rep1; Danio rerio; RNA Seq,GSM8703886 r1,GSM8703886,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_1_R1.fastq.gz EIB202_1_R2.fastq.gz,fastq fastq,6634863292.0,21969746.0,GSM8703886 r1,0:151 1:151,A:1708949626;C:1589664250;G:1615939413;T:1720201415;N:108588,151,151,,,1708949626,1589664250,1615939413,1720201415,108588,SRX27211964,SRS23661287,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34497,SRR31852183,SRX27211963,SRS23661286,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  mock  rep3,GSM8703885,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  mock  rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703885,GSM8703885: Zebrafish  mock  rep3; Danio rerio; RNA Seq,GSM8703885 r1,GSM8703885,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_3_R1.fastq.gz Mock_3_R2.fastq.gz,fastq fastq,6938479596.0,22975098.0,GSM8703885 r1,0:151 1:151,A:1771058080;C:1670207033;G:1705035413;T:1792066207;N:112863,151,151,,,1771058080,1670207033,1705035413,1792066207,112863,SRX27211963,SRS23661286,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34498,SRR31852184,SRX27211962,SRS23661285,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  mock  rep2,GSM8703884,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  mock  rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703884,GSM8703884: Zebrafish  mock  rep2; Danio rerio; RNA Seq,GSM8703884 r1,GSM8703884,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_2_R1.fastq.gz Mock_2_R2.fastq.gz,fastq fastq,7374531658.0,24418979.0,GSM8703884 r1,0:151 1:151,A:1885070518;C:1779385428;G:1810157081;T:1899798486;N:120145,151,151,,,1885070518,1779385428,1810157081,1899798486,120145,SRX27211962,SRS23661285,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34499,SRR31852185,SRX27211961,SRS23661284,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  mock  rep1,GSM8703883,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  mock  rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703883,GSM8703883: Zebrafish  mock  rep1; Danio rerio; RNA Seq,GSM8703883 r1,GSM8703883,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_1_R1.fastq.gz Mock_1_R2.fastq.gz,fastq fastq,6563252448.0,21732624.0,GSM8703883 r1,0:151 1:151,A:1759569033;C:1514211809;G:1536003223;T:1753362072;N:106311,151,151,,,1759569033,1514211809,1536003223,1753362072,106311,SRX27211961,SRS23661284,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
38059,SRR1524245,SRX661010,SRS665985,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish intestine,Zebrafish intestine,F Dr 9,,strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish intestine,F Dr 9,F Dr 9,Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP044781,,,F_Dr_9_GCCAAT_L005_R2.fastq.gz F_Dr_9_GCCAAT_L005_R1.fastq.gz,fastq fastq,8637468200.0,43187341.0,F Dr 9 files,0:100 1:100,A:2270309093;C:2039596980;G:2056249938;T:2263331787;N:7980402,100,100,,,2270309093,2039596980,2056249938,2263331787,7980402,SRX661010,SRS665985,SRA176464,INRA|Fish Physiology and Genomics,INRA PhyloFish,2,0.94661,0.94511,0.06033,0.06049,0.75743,0.75747,0.43604,0.43901,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,France,2015-07-24,Adult,Adult,Gut,Digestive System
38269,SRR1609746,SRX730399,SRS719620,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine10,GSM1523041,,source name:intestine|tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf,intestine10,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf,GSM1523041,GSM1523041: intestine10; Danio rerio; RNA Seq,GSM1523041,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523041,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine10_2.fq.gz intestine10_1.fq.gz,fastq fastq,3638953000.0,18194765.0,GSM1523041 r1,0:100 1:100,A:944286084;C:877180113;G:870958371;T:946463708;N:64724,100,100,,,944286084,877180113,870958371,946463708,64724,SRX730399,SRS719620,SRA189240,GEO,Shanghai Ocean University,2,0.95871,0.95555,0.03654,0.03737,0.77546,0.77597,0.49972,0.50867,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
38270,SRR1609745,SRX730398,SRS719619,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine18,GSM1523040,,source name:intestine|tissue:intestine|temperature:18°C|strain:Tubingen|age:6 mpf,intestine18,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:18°C|strain:Tubingen|age:6 mpf,GSM1523040,GSM1523040: intestine18; Danio rerio; RNA Seq,GSM1523040,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523040,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine18_1.fq.gz intestine18_2.fq.gz,fastq fastq,3870426800.0,19352134.0,GSM1523040 r1,0:100 1:100,A:1034436410;C:900862332;G:899347839;T:1035707094;N:73125,100,100,,,1034436410,900862332,899347839,1035707094,73125,SRX730398,SRS719619,SRA189240,GEO,Shanghai Ocean University,2,0.93279,0.92997,0.0455,0.04571,0.76152,0.76228,0.44545,0.44882,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
38271,SRR1609744,SRX730397,SRS719618,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine28,GSM1523039,,source name:intestine|tissue:intestine|temperature:28°C|strain:Tubingen|age:6 mpf,intestine28,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:28°C|strain:Tubingen|age:6 mpf,GSM1523039,GSM1523039: intestine28; Danio rerio; RNA Seq,GSM1523039,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine28_1.fq.gz intestine28_2.fq.gz,fastq fastq,3710350200.0,18551751.0,GSM1523039 r1,0:100 1:100,A:987499090;C:870092319;G:865419689;T:987267641;N:71461,100,100,,,987499090,870092319,865419689,987267641,71461,SRX730397,SRS719618,SRA189240,GEO,Shanghai Ocean University,2,0.94613,0.94058,0.04736,0.04784,0.7599,0.76288,0.51653,0.51797,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
41072,SRR3655801,SRX1836012,SRS1495476,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,GSM2195935,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195935,GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq,GSM2195935,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS410.fastq.gz,fastq,1402184556.0,18692635.0,GSM2195935 r1,0:75.01 1:0,A:363262740;C:326626075;G:322630446;T:389582075;N:83220,75,0,,,363262740,326626075,322630446,389582075,83220,SRX1836012,SRS1495476,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92115,,0.08008,,0.7389,,0.52691,,73,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41073,SRR3655802,SRX1836012,SRS1495476,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,GSM2195935,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195935,GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq,GSM2195935,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS410.fastq.gz,fastq,3450884531.0,46005067.0,GSM2195935 r2,0:75.01 1:0,A:874448337;C:808236306;G:797225707;T:970673048;N:301133,75,0,,,874448337,808236306,797225707,970673048,301133,SRX1836012,SRS1495476,SRA432774,GEO,Children's Hospital Los Angeles,1,0.93035,,0.08192,,0.73271,,0.52273,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41074,SRR3655799,SRX1836011,SRS1495475,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,GSM2195934,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195934,GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq,GSM2195934,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195934,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS409.fastq.gz,fastq,1422635421.0,18963577.0,GSM2195934 r1,0:75.02 1:0,A:362173330;C:332883466;G:329078937;T:398420070;N:79618,75,0,,,362173330,332883466,329078937,398420070,79618,SRX1836011,SRS1495475,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92474,,0.07466,,0.73423,,0.50871,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41075,SRR3655800,SRX1836011,SRS1495475,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,GSM2195934,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195934,GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq,GSM2195934,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195934,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS409.fastq.gz,fastq,3549432159.0,47315580.0,GSM2195934 r2,0:75.02 1:0,A:893492844;C:832741437;G:822208498;T:1000698758;N:290622,75,0,,,893492844,832741437,822208498,1000698758,290622,SRX1836011,SRS1495475,SRA432774,GEO,Children's Hospital Los Angeles,1,0.93197,,0.07554,,0.73109,,0.50825,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41076,SRR3655797,SRX1836010,SRS1495474,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,GSM2195933,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195933,GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq,GSM2195933,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195933,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS408.fastq.gz,fastq,1400640841.0,18670640.0,GSM2195933 r1,0:75.02 1:0,A:363544908;C:324586412;G:320620988;T:391797091;N:91442,75,0,,,363544908,324586412,320620988,391797091,91442,SRX1836010,SRS1495474,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92971,,0.10926,,0.73016,,0.51418,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41077,SRR3655798,SRX1836010,SRS1495474,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,GSM2195933,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195933,GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq,GSM2195933,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195933,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS408.fastq.gz,fastq,1400640841.0,18670640.0,GSM2195933 r2,0:75.02 1:0,A:363544908;C:324586412;G:320620988;T:391797091;N:91442,75,0,,,363544908,324586412,320620988,391797091,91442,SRX1836010,SRS1495474,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92977,,0.10933,,0.73008,,0.51355,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41078,SRR3655795,SRX1836009,SRS1495472,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,GSM2195932,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195932,GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq,GSM2195932,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS383.fastq.gz,fastq,1510741670.0,20138480.0,GSM2195932 r1,0:75.02 1:0,A:374411447;C:361418430;G:359803924;T:415021333;N:86536,75,0,,,374411447,361418430,359803924,415021333,86536,SRX1836009,SRS1495472,SRA432774,GEO,Children's Hospital Los Angeles,1,0.94789,,0.05269,,0.77753,,0.53939,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41079,SRR3655796,SRX1836009,SRS1495472,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,GSM2195932,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195932,GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq,GSM2195932,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS383.fastq.gz,fastq,3623681121.0,48303841.0,GSM2195932 r2,0:75.02 1:0,A:881893112;C:869893713;G:867139931;T:1004485159;N:269206,75,0,,,881893112,869893713,867139931,1004485159,269206,SRX1836009,SRS1495472,SRA432774,GEO,Children's Hospital Los Angeles,1,0.95546,,0.05225,,0.77218,,0.53519,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41080,SRR3655793,SRX1836008,SRS1495473,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,GSM2195931,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195931,GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq,GSM2195931,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS381.fastq.gz,fastq,1348860046.0,17985061.0,GSM2195931 r1,0:75.00 1:0,A:350940564;C:313266568;G:309387786;T:375159308;N:105820,75,0,,,350940564,313266568,309387786,375159308,105820,SRX1836008,SRS1495473,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92348,,0.06356,,0.77252,,0.52707,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41081,SRR3655794,SRX1836008,SRS1495473,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,GSM2195931,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195931,GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq,GSM2195931,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS381.fastq.gz,fastq,3298786881.0,43979655.0,GSM2195931 r2,0:75.01 1:0,A:829523096;C:775146066;G:763427556;T:930352935;N:337228,75,0,,,829523096,775146066,763427556,930352935,337228,SRX1836008,SRS1495473,SRA432774,GEO,Children's Hospital Los Angeles,1,0.9361,,0.06336,,0.76353,,0.54746,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41082,SRR3655791,SRX1836007,SRS1495471,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,GSM2195930,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195930,GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq,GSM2195930,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS380.fastq.gz,fastq,1448364484.0,19307379.0,GSM2195930 r1,0:75.02 1:0,A:359052072;C:343824905;G:344804667;T:400589883;N:92957,75,0,,,359052072,343824905,344804667,400589883,92957,SRX1836007,SRS1495471,SRA432774,GEO,Children's Hospital Los Angeles,1,0.94277,,0.05284,,0.77881,,0.57769,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41083,SRR3655792,SRX1836007,SRS1495471,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,GSM2195930,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195930,GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq,GSM2195930,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS380.fastq.gz,fastq,3599154025.0,47976708.0,GSM2195930 r2,0:75.02 1:0,A:875615940;C:857379635;G:859609503;T:1006260031;N:288916,75,0,,,875615940,857379635,859609503,1006260031,288916,SRX1836007,SRS1495471,SRA432774,GEO,Children's Hospital Los Angeles,1,0.95037,,0.0525,,0.77147,,0.5711,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41575,SRR5045902,SRX2368488,SRS1814332,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutCV 2,GSM2401374,,source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutCV 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401374,GSM2401374: MutCV 2; Danio rerio; RNA Seq,GSM2401374,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401374,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutCV_2.fastq,fastq,3876906576.0,76017776.0,GSM2401374 r1,0:51 1:0,A:957781980;C:915286453;G:859927041;T:1143804372;N:106730,51,0,,,957781980,915286453,859927041,1143804372,106730,SRX2368488,SRS1814332,SRA497672,GEO,Duke University School of Medicine,1,0.96196,,0.11375,,0.70887,,0.53406,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41576,SRR5045901,SRX2368487,SRS1814330,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutCV 1,GSM2401373,,source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutCV 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401373,GSM2401373: MutCV 1; Danio rerio; RNA Seq,GSM2401373,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401373,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutCV_1.fastq,fastq,3835824444.0,75212244.0,GSM2401373 r1,0:51 1:0,A:946407906;C:904393791;G:851683286;T:1133241327;N:98134,51,0,,,946407906,904393791,851683286,1133241327,98134,SRX2368487,SRS1814330,SRA497672,GEO,Duke University School of Medicine,1,0.95795,,0.11761,,0.70481,,0.53357,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41577,SRR5045900,SRX2368486,SRS1814331,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutGF 2,GSM2401372,,source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutGF 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401372,GSM2401372: MutGF 2; Danio rerio; RNA Seq,GSM2401372,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401372,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutGF_2.fastq,fastq,3299677866.0,64699566.0,GSM2401372 r1,0:51 1:0,A:809247440;C:784035543;G:731742820;T:974610541;N:41522,51,0,,,809247440,784035543,731742820,974610541,41522,SRX2368486,SRS1814331,SRA497672,GEO,Duke University School of Medicine,1,0.96247,,0.1049,,0.74034,,0.5525,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41578,SRR5045899,SRX2368485,SRS1814329,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutGF 1,GSM2401371,,source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutGF 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401371,GSM2401371: MutGF 1; Danio rerio; RNA Seq,GSM2401371,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401371,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutGF_1.fastq,fastq,3734921199.0,73233749.0,GSM2401371 r1,0:51 1:0,A:923493830;C:879193170;G:840678282;T:1091454504;N:101413,51,0,,,923493830,879193170,840678282,1091454504,101413,SRX2368485,SRS1814329,SRA497672,GEO,Duke University School of Medicine,1,0.96328,,0.1099,,0.73492,,0.50455,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41579,SRR5045898,SRX2368484,SRS1814328,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 3,GSM2401370,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 3,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401370,GSM2401370: WTCV 3; Danio rerio; RNA Seq,GSM2401370,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_3.fastq,fastq,3928418412.0,77027812.0,GSM2401370 r1,0:51 1:0,A:966197912;C:939595492;G:912123411;T:1110393846;N:107751,51,0,,,966197912,939595492,912123411,1110393846,107751,SRX2368484,SRS1814328,SRA497672,GEO,Duke University School of Medicine,1,0.97188,,0.08862,,0.7357,,0.53339,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41580,SRR5045897,SRX2368483,SRS1814327,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 2,GSM2401369,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401369,GSM2401369: WTCV 2; Danio rerio; RNA Seq,GSM2401369,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_2.fastq,fastq,3782941473.0,74175323.0,GSM2401369 r1,0:51 1:0,A:928563733;C:910471684;G:872137892;T:1071716851;N:51313,51,0,,,928563733,910471684,872137892,1071716851,51313,SRX2368483,SRS1814327,SRA497672,GEO,Duke University School of Medicine,1,0.97097,,0.09668,,0.74255,,0.55455,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41581,SRR5045896,SRX2368482,SRS1814326,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 1,GSM2401368,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401368,GSM2401368: WTCV 1; Danio rerio; RNA Seq,GSM2401368,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_1.fastq,fastq,3643146954.0,71434254.0,GSM2401368 r1,0:51 1:0,A:877377891;C:875020597;G:839793450;T:1050862579;N:92437,51,0,,,877377891,875020597,839793450,1050862579,92437,SRX2368482,SRS1814326,SRA497672,GEO,Duke University School of Medicine,1,0.9683,,0.08514,,0.73525,,0.55486,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41582,SRR5045895,SRX2368481,SRS1814325,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 3,GSM2401367,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 3,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401367,GSM2401367: WTGF 3; Danio rerio; RNA Seq,GSM2401367,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401367,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_3.fastq,fastq,3462802386.0,67898086.0,GSM2401367 r1,0:51 1:0,A:843407439;C:830117704;G:803633976;T:985548502;N:94765,51,0,,,843407439,830117704,803633976,985548502,94765,SRX2368481,SRS1814325,SRA497672,GEO,Duke University School of Medicine,1,0.97202,,0.08623,,0.75939,,0.56558,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41583,SRR5045894,SRX2368480,SRS1814324,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 2,GSM2401366,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401366,GSM2401366: WTGF 2; Danio rerio; RNA Seq,GSM2401366,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401366,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_2.fastq,fastq,3699149799.0,72532349.0,GSM2401366 r1,0:51 1:0,A:907425678;C:884609705;G:855651232;T:1051368070;N:95114,51,0,,,907425678,884609705,855651232,1051368070,95114,SRX2368480,SRS1814324,SRA497672,GEO,Duke University School of Medicine,1,0.96861,,0.08856,,0.75223,,0.55327,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41584,SRR5045893,SRX2368479,SRS1814323,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 1,GSM2401365,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401365,GSM2401365: WTGF 1; Danio rerio; RNA Seq,GSM2401365,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401365,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_1.fastq,fastq,3948593247.0,77423397.0,GSM2401365 r1,0:51 1:0,A:951060123;C:949871425;G:909862458;T:1137745436;N:53805,51,0,,,951060123,949871425,909862458,1137745436,53805,SRX2368479,SRS1814323,SRA497672,GEO,Duke University School of Medicine,1,0.97252,,0.08483,,0.74418,,0.54605,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41844,SRR5259817,SRX2564548,SRS1981207,SRP099850,PRJNA374872,Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish],GSE94933,Other,We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish,parent bioproject:PRJNA374867,pubmed:28850571,,zIEC3 mRNA,GSM2492108,,tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,zIEC3 mRNA,Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information,Intestinal Epithelial Cells RNA seq,,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets,strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,GSM2492108,GSM2492108: zIEC3 mRNA; Danio rerio; RNA Seq,GSM2492108,,1,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,GEO Accession:GSM2492108,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP099850,,,ZIEC3_GCCAAT_L001_R2_001.fastq.gz ZIEC3_GCCAAT_L001_R1_001.fastq.gz,fastq fastq,2644689216.0,27548846.0,GSM2492108 r1,0:48 1:48,A:687890725;C:632255900;G:620389531;T:703494916;N:658144,48,48,,,687890725,632255900,620389531,703494916,658144,SRX2564548,SRS1981207,SRA538156,GEO,"John Rawls, Duke University",2,0.87587,0.87862,0.06582,0.06632,0.73931,0.73878,0.53496,0.53653,48,48,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-02-15,Adult,Adult,Gut,Digestive System