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
9166,ERR2788341,ERX2797590,ERS2709706,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7292228,SAMEA4890710,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female  1 male|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7292228 p,5149STDY7292228 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7292228.bam 5149STDY7292228.bam.bai,bam bam,37970494940.0,387454030.0,E MTAB 7159:5149STDY7292228,0:98,A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108,98,,,,11476520187,7571635167,8189594199,10701044279,31701108,ERX2797590,ERS2709706,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.87568,,0.2122,,0.82582,,0.5259,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9167,ERR2788340,ERX2797589,ERS2709705,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274848,SAMEA4890709,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274848 p,5149STDY7274848 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274848.bam 5149STDY7274848.bam.bai,bam bam,34517322840.0,352217580.0,E MTAB 7159:5149STDY7274848,0:98,A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273,98,,,,10635243399,6658515314,7525079510,9695995344,2489273,ERX2797589,ERS2709705,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.86206,,0.18065,,0.83514,,0.53609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9168,ERR2788339,ERX2797588,ERS2709704,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274847,SAMEA4890708,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274847 p,5149STDY7274847 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274847.bam 5149STDY7274847.bam.bai,bam bam,34467649678.0,351710711.0,E MTAB 7159:5149STDY7274847,0:98,A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266,98,,,,10609988948,6722093635,7464497879,9667814950,3254266,ERX2797588,ERS2709704,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88751,,0.21835,,0.83771,,0.53927,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9169,ERR2788338,ERX2797587,ERS2709703,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274846,SAMEA4890707,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274846 p,5149STDY7274846 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274846.bam 5149STDY7274846.bam.bai,bam bam,35052538472.0,357678964.0,E MTAB 7159:5149STDY7274846,0:98,A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277,98,,,,10698116265,6858102477,7626019661,9866905792,3394277,ERX2797587,ERS2709703,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88916,,0.21537,,0.83802,,0.5336,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
25135,SRR25649156,SRX21375305,SRS18618397,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X8,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X8,18689X8,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X8_R1.fastq.gz 18689X8_R2.fastq.gz,fastq fastq,8163984120.0,27033060.0,18689X8 R1.fastq.gz,0:151 1:151,A:1900143724;C:2183735704;G:2147710753;T:1932229591;N:164348,151,151,,,1900143724,2183735704,2147710753,1932229591,164348,SRX21375305,SRS18618397,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89288,0.89479,0.20193,0.20116,0.79072,0.79352,0.57246,0.56409,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25136,SRR25649157,SRX21375304,SRS18618396,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X15,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X15,19629X15,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X15_R2.fastq.gz 19629X15_R1.fastq.gz,fastq fastq,10277997106.0,34033103.0,19629X15 R1.fastq.gz,0:151 1:151,A:2798108841;C:2341310321;G:2438634645;T:2699729301;N:213998,151,151,,,2798108841,2341310321,2438634645,2699729301,213998,SRX21375304,SRS18618396,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90655,0.90714,0.18082,0.18027,0.72803,0.72953,0.45722,0.45335,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25137,SRR25649158,SRX21375303,SRS18618395,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X14,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 3|replicate:T2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X14,19629X14,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X14_R1.fastq.gz 19629X14_R2.fastq.gz,fastq fastq,10921707086.0,36164593.0,19629X14 R1.fastq.gz,0:151 1:151,A:2969229092;C:2484790148;G:2595052715;T:2872407360;N:227771,151,151,,,2969229092,2484790148,2595052715,2872407360,227771,SRX21375303,SRS18618395,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90015,0.90211,0.19548,0.19546,0.72997,0.73131,0.53978,0.54998,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25138,SRR25649159,SRX21375302,SRS18618394,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X13,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X13,19629X13,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X13_R1.fastq.gz 19629X13_R2.fastq.gz,fastq fastq,10019262230.0,33176365.0,19629X13 R1.fastq.gz,0:151 1:151,A:2732766602;C:2270429150;G:2391166434;T:2624690350;N:209694,151,151,,,2732766602,2270429150,2391166434,2624690350,209694,SRX21375302,SRS18618394,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90381,0.90536,0.18425,0.18388,0.72681,0.72936,0.48627,0.49398,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25139,SRR25649160,SRX21375301,SRS18618393,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X12,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X12,19629X12,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X12_R1.fastq.gz 19629X12_R2.fastq.gz,fastq fastq,11078632326.0,36684213.0,19629X12 R1.fastq.gz,0:151 1:151,A:2995473302;C:2550446088;G:2653594689;T:2878887522;N:230725,151,151,,,2995473302,2550446088,2653594689,2878887522,230725,SRX21375301,SRS18618393,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91101,0.91121,0.16145,0.16142,0.70274,0.70498,0.47852,0.48788,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25140,SRR25649161,SRX21375300,SRS18618392,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X11,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X11,19629X11,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X11_R1.fastq.gz 19629X11_R2.fastq.gz,fastq fastq,10957183630.0,36282065.0,19629X11 R1.fastq.gz,0:151 1:151,A:2987773085;C:2485587980;G:2603747193;T:2879845340;N:230032,151,151,,,2987773085,2485587980,2603747193,2879845340,230032,SRX21375300,SRS18618392,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91198,0.91301,0.20992,0.20926,0.73044,0.73316,0.44301,0.43596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25141,SRR25649162,SRX21375299,SRS18618390,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X10,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X10,19629X10,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X10_R1.fastq.gz 19629X10_R2.fastq.gz,fastq fastq,9549065142.0,31619421.0,19629X10 R1.fastq.gz,0:151 1:151,A:2603092155;C:2167963952;G:2264536965;T:2513273275;N:198795,151,151,,,2603092155,2167963952,2264536965,2513273275,198795,SRX21375299,SRS18618390,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.92549,0.92615,0.16176,0.15925,0.7683,0.76926,0.3093,0.30927,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25144,SRR25649165,SRX21375296,SRS18618388,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X6,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X6,18843X6,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X6_R1.fastq.gz 18843X6_R2.fastq.gz,fastq fastq,8690806510.0,28777505.0,18843X6 R1.fastq.gz,0:151 1:151,A:2346658651;C:2002583855;G:2108507319;T:2232918222;N:138463,151,151,,,2346658651,2002583855,2108507319,2232918222,138463,SRX21375296,SRS18618388,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91741,0.91785,0.21796,0.21778,0.6971,0.70102,0.49123,0.51016,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25147,SRR25649168,SRX21375293,SRS18618385,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X3,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X3,18843X3,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X3_R1.fastq.gz 18843X3_R2.fastq.gz,fastq fastq,9351018676.0,30963638.0,18843X3 R1.fastq.gz,0:151 1:151,A:2555870224;C:2133006230;G:2246501165;T:2415491618;N:149439,151,151,,,2555870224,2133006230,2246501165,2415491618,149439,SRX21375293,SRS18618385,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91594,0.91512,0.21678,0.21621,0.72719,0.73117,0.52961,0.53327,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25149,SRR25649170,SRX21375291,SRS18618383,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X9,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X9,19629X9,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X9_R1.fastq.gz 19629X9_R2.fastq.gz,fastq fastq,12342730940.0,40869970.0,19629X9 R1.fastq.gz,0:151 1:151,A:3339874828;C:2828928610;G:2945452577;T:3228218292;N:256633,151,151,,,3339874828,2828928610,2945452577,3228218292,256633,SRX21375291,SRS18618383,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90738,0.8127,0.19825,0.17409,0.73385,0.74659,0.54306,0.55304,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25151,SRR25649172,SRX21375289,SRS18618381,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X5,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X5,18689X5,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X5_R1.fastq.gz 18689X5_R2.fastq.gz,fastq fastq,8136028886.0,26940493.0,18689X5 R1.fastq.gz,0:151 1:151,A:2015403368;C:2051480513;G:2023331135;T:2045661742;N:152128,151,151,,,2015403368,2051480513,2023331135,2045661742,152128,SRX21375289,SRS18618381,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88067,0.88216,0.24575,0.2425,0.75018,0.75073,0.59361,0.61451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25154,SRR25649175,SRX21375286,SRS18618378,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X9,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X9,18843X9,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X9_R1.fastq.gz 18843X9_R2.fastq.gz,fastq fastq,8819654206.0,29204153.0,18843X9 R1.fastq.gz,0:151 1:151,A:2383706177;C:2044504407;G:2140881818;T:2250422256;N:139548,151,151,,,2383706177,2044504407,2140881818,2250422256,139548,SRX21375286,SRS18618378,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90385,0.90437,0.21274,0.21235,0.72604,0.73164,0.52888,0.52909,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25157,SRR25649178,SRX21375283,SRS18618375,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X7,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X7,18689X7,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X7_R1.fastq.gz 18689X7_R2.fastq.gz,fastq fastq,8986035368.0,29755084.0,18689X7 R1.fastq.gz,0:151 1:151,A:2169723143;C:2326462981;G:2292317481;T:2197350043;N:181720,151,151,,,2169723143,2326462981,2292317481,2197350043,181720,SRX21375283,SRS18618375,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89254,0.89285,0.22562,0.22356,0.74911,0.75089,0.6409,0.65585,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25160,SRR25649181,SRX21375280,SRS18618372,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X8,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X8,19629X8,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X8_R2.fastq.gz 19629X8_R1.fastq.gz,fastq fastq,10758135430.0,35622965.0,19629X8 R1.fastq.gz,0:151 1:151,A:2991372806;C:2398155523;G:2517276916;T:2851104238;N:225947,151,151,,,2991372806,2398155523,2517276916,2851104238,225947,SRX21375280,SRS18618372,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88839,0.89055,0.23357,0.23344,0.72592,0.72851,0.53343,0.53081,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25161,SRR25649182,SRX21375279,SRS18618371,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X7,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X7,19629X7,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X7_R1.fastq.gz 19629X7_R2.fastq.gz,fastq fastq,11738178884.0,38868142.0,19629X7 R1.fastq.gz,0:151 1:151,A:3192358555;C:2674045852;G:2784070515;T:3087458659;N:245303,151,151,,,3192358555,2674045852,2784070515,3087458659,245303,SRX21375279,SRS18618371,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.9074,0.90829,0.20853,0.20916,0.74115,0.74369,0.53704,0.55385,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,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
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
34517,SRR32044795,SRX27393953,SRS23824014,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 3,I,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 3,Cr+VC 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz,fastq fastq,6773536558.0,22428929.0,Cr+VC 3.R1.raw.fastq.gz,0:151 1:151,A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278,151,151,,,1792253952,1581454013,1629330621,1770470694,27278,SRX27393953,SRS23824014,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34518,SRR32044796,SRX27393952,SRS23824013,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 2,H,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 2,Cr+VC 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz,fastq fastq,7449518862.0,24667281.0,Cr+VC 2.R1.raw.fastq.gz,0:151 1:151,A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119,151,151,,,1969693675,1748150730,1771267240,1960378098,29119,SRX27393952,SRS23824013,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34519,SRR32044797,SRX27393951,SRS23824012,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 1,G,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 1,Cr+VC 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options:  doNotUseSharq,Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq,fastq fastq,6865491179.0,45466829.0,Cr+VC 1.R1.raw.fastq.gz,0:151,A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474,151,,,,1830069736,1600281531,1626303427,1808809011,27474,SRX27393951,SRS23824012,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34520,SRR32044798,SRX27393950,SRS23824011,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 3,F,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 3,Cr 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz,fastq fastq,6069804078.0,20098689.0,Cr 3.R1.raw.fastq.gz,0:151 1:151,A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079,151,151,,,1603886661,1431213970,1440806224,1593873144,24079,SRX27393950,SRS23824011,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34521,SRR32044799,SRX27393949,SRS23824010,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 2,E,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 2,Cr 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options:  doNotUseSharq,Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq,fastq fastq,8327156985.0,55146735.0,Cr 2.R1.raw.fastq.gz,0:151,A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145,151,,,,2181317777,1974793526,2003240106,2167771431,34145,SRX27393949,SRS23824010,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34522,SRR32044800,SRX27393948,SRS23824009,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 1,D,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 1,Cr 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz,fastq fastq,7322067614.0,24245257.0,Cr 1.R1.raw.fastq.gz,0:151 1:151,A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557,151,151,,,1927213281,1727973559,1748866497,1917985720,28557,SRX27393948,SRS23824009,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34523,SRR32044801,SRX27393947,SRS23824008,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 3,C,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 3,Con 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz,fastq fastq,10329187314.0,34202607.0,Con 3.R1.raw.fastq.gz,0:151 1:151,A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354,151,151,,,2805764955,2343400161,2421657823,2758323021,41354,SRX27393947,SRS23824008,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34524,SRR32044802,SRX27393946,SRS23824007,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 2,B,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 2,Con 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz,fastq fastq,10789961398.0,35728349.0,Con 2.R1.raw.fastq.gz,0:151 1:151,A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353,151,151,,,2983305704,2396592872,2488165589,2921853880,43353,SRX27393946,SRS23824007,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34525,SRR32044803,SRX27393945,SRS23824006,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 1,A,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 1,Con 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz,fastq fastq,7118179260.0,23570130.0,Con 1.R1.raw.fastq.gz,0:151 1:151,A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275,151,151,,,1874284939,1673861890,1718740497,1851263659,28275,SRX27393945,SRS23824006,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,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
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
41845,SRR5259816,SRX2564547,SRS1981208,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,,zIEC2 mRNA,GSM2492107,,tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,zIEC2 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,GSM2492107,GSM2492107: zIEC2 mRNA; Danio rerio; RNA Seq,GSM2492107,,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:GSM2492107,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP099850,,,ZIEC2_GCCAAT_L005_R1_001.fastq.gz ZIEC2_GCCAAT_L005_R2_001.fastq.gz,fastq fastq,1785594816.0,18599946.0,GSM2492107 r1,0:48 1:48,A:466092820;C:422828003;G:420238032;T:476324795;N:111166,48,48,,,466092820,422828003,420238032,476324795,111166,SRX2564547,SRS1981208,SRA538156,GEO,"John Rawls, Duke University",2,0.85545,0.86359,0.08337,0.08488,0.74635,0.74677,0.52663,0.53064,48,48,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
41846,SRR5259815,SRX2564546,SRS1981206,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,,zIEC1 mRNA,GSM2492106,,tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,zIEC1 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,GSM2492106,GSM2492106: zIEC1 mRNA; Danio rerio; RNA Seq,GSM2492106,,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:GSM2492106,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP099850,,,ZIEC1_CGATGT_L004_R1_001.fastq.gz ZIEC1_CGATGT_L004_R2_001.fastq.gz,fastq fastq,1953396576.0,20347881.0,GSM2492106 r1,0:48 1:48,A:510243495;C:461085497;G:464477553;T:517509152;N:80879,48,48,,,510243495,461085497,464477553,517509152,80879,SRX2564546,SRS1981206,SRA538156,GEO,"John Rawls, Duke University",2,0.87991,0.88564,0.09576,0.0974,0.74789,0.74909,0.54326,0.54368,48,48,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
52131,SRR8944754,SRX5724887,SRS4662952,SRP193452,PRJNA534016,fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome,PRJNA534016,Other,In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.,,,In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.,fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome,intestinal transcriptome sequencing of fabp2 gene KO and WT zebrafish,,isolate:fabp2 gene KO and WT zebrafish|dev stage:adult|sex:not collected|tissue:intestine|collected by:Yan Zhao|collection date:2017 10|geo loc name:China: Wuhan city  Hubei province|sample type:tissue sample|BioSampleModel:Model organism or animal,,,,,,,,,intestinal transcritome sequencing,fabp2 gene KO Danio rerio,fabp2 gene KO Danio rerio,Total RNAs were extracted from the intestine of experimental fish using Trizol. The construction of the cDNA library and sequencing were performed using Illumina NovaSeq 6000 HiSeq 2000 platform Illumina  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP193452,,,KO1_1.fastq.gz KO2_2.fastq.gz KO2_1.fastq.gz KO1_2.fastq.gz,fastq fastq fastq fastq,21269908500.0,70899695.0,KO1 1.fastq.gz,0:150 1:150,A:5602268133;C:4968099632;G:4965298378;T:5733027255;N:1215102,150,150,,,5602268133,4968099632,4965298378,5733027255,1215102,SRX5724887,SRS4662952,SRA878388,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,2,0.92003,0.92121,0.03272,0.03273,0.78488,0.78859,0.49044,0.48398,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-04-23,Adult,Adult,Gut,Digestive System
52132,SRR8944755,SRX5724886,SRS4662952,SRP193452,PRJNA534016,fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome,PRJNA534016,Other,In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.,,,In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.,fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome,intestinal transcriptome sequencing of fabp2 gene KO and WT zebrafish,,isolate:fabp2 gene KO and WT zebrafish|dev stage:adult|sex:not collected|tissue:intestine|collected by:Yan Zhao|collection date:2017 10|geo loc name:China: Wuhan city  Hubei province|sample type:tissue sample|BioSampleModel:Model organism or animal,,,,,,,,,intestinal transcritome sequencing,wild type Danio rerio,wild type Danio rerio,Total RNAs were extracted from the intestine of experimental fish using Trizol. The construction of the cDNA library and sequencing were performed using Illumina NovaSeq 6000 HiSeq 2001 platform Illumina  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP193452,,,WT1_1.fastq.gz WT1_2.fastq.gz WT2_1.fastq.gz WT2_2.fastq.gz,fastq fastq fastq fastq,23433575100.0,78111917.0,WT1 1.fastq.gz,0:150 1:150,A:6211885445;C:5476158510;G:5474363796;T:6269801731;N:1365618,150,150,,,6211885445,5476158510,5474363796,6269801731,1365618,SRX5724886,SRS4662952,SRA878388,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,2,0.92141,0.92214,0.04124,0.04142,0.77664,0.78182,0.5318,0.52116,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-04-23,Adult,Adult,Gut,Digestive System
52338,SRR9141302,SRX5914456,SRS4832644,SRP199735,PRJNA545244,Zebrafish transcriptome data,PRJNA545244,Other,Heavy metals stimulate zebrafish,,,,,Drt1 2 aliquot,,isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female gut,Drt1 2,Drt1 2,Gene expression in zebrafish stimulated by heavy metals,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP199735,,,Drt1-2 (pooling35-GCCAAT_HY2FYCCXY_L8_1.fq and pooling35-GCCAAT_HY2FYCCXY_L8_2.fq).gz,fastq,4010314800.0,26735432.0,Drt1 2 pooling35 GCCAAT HY2FYCCXY L8 1.fq and pooling35 GCCAAT HY2FYCCXY L8 2.fq.gz,0:0 1:150,A:1109402697;C:898932519;G:975504514;T:1026302103;N:172967,0,150,,,1109402697,898932519,975504514,1026302103,172967,SRX5914456,SRS4832644,SRA891446,Kunming University of Science and Technology|College of Life Science,Kunming University of Science and Technology,1,0.92372,,0.03616,,0.74588,,0.49008,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-29,Adult,Adult,Gut,Digestive System
52339,SRR9141303,SRX5914455,SRS4832643,SRP199735,PRJNA545244,Zebrafish transcriptome data,PRJNA545244,Other,Heavy metals stimulate zebrafish,,,,,Drt1 3 aliquot,,isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female gut,Drt1 3,Drt1 3,Gene expression in zebrafish stimulated by heavy metals,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP199735,,,Drt1-3 (pooling35-CAGATC_HY2FYCCXY_L8_1.fq and pooling35-CAGATC_HY2FYCCXY_L8_2.fq).gz,fastq,3497539200.0,23316928.0,Drt1 3 pooling35 CAGATC HY2FYCCXY L8 1.fq and pooling35 CAGATC HY2FYCCXY L8 2.fq.gz,0:0 1:150,A:965958483;C:783630086;G:850473225;T:897324973;N:152433,0,150,,,965958483,783630086,850473225,897324973,152433,SRX5914455,SRS4832643,SRA891446,Kunming University of Science and Technology|College of Life Science,Kunming University of Science and Technology,1,0.92356,,0.03568,,0.7417,,0.48985,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-29,Adult,Adult,Gut,Digestive System
52340,SRR9141304,SRX5914454,SRS4832642,SRP199735,PRJNA545244,Zebrafish transcriptome data,PRJNA545244,Other,Heavy metals stimulate zebrafish,,,,,Drck3 aliquot,,isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female gut,Drck3,Drck3,Gene expression in zebrafish stimulated by heavy metals,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP199735,,,Drck3 (pooling35-TAGCTT_HY2FYCCXY_L8_1.fq and pooling35-TAGCTT_HY2FYCCXY_L8_2.fq).gz,fastq,4199739150.0,27998261.0,Drck3 pooling35 TAGCTT HY2FYCCXY L8 1.fq and pooling35 TAGCTT HY2FYCCXY L8 2.fq.gz,0:0 1:150,A:1173351504;C:941132248;G:1019438569;T:1065634216;N:182613,0,150,,,1173351504,941132248,1019438569,1065634216,182613,SRX5914454,SRS4832642,SRA891446,Kunming University of Science and Technology|College of Life Science,Kunming University of Science and Technology,1,0.92976,,0.0377,,0.71709,,0.48608,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-29,Adult,Adult,Gut,Digestive System
52341,SRR9141305,SRX5914453,SRS4832641,SRP199735,PRJNA545244,Zebrafish transcriptome data,PRJNA545244,Other,Heavy metals stimulate zebrafish,,,,,Drt1 1 aliquot,,isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female gut,Drt1 1,Drt1 1,Gene expression in zebrafish stimulated by heavy metals,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP199735,,,Drt1-1 (pooling35-ACAGTG_HY2FYCCXY_L8_1.fq and pooling35-ACAGTG_HY2FYCCXY_L8_2.fq).gz,fastq,3657007500.0,24380050.0,Drt1 1 pooling35 ACAGTG HY2FYCCXY L8 1.fq and pooling35 ACAGTG HY2FYCCXY L8 2.fq.gz,0:150 1:0,A:963212012;C:848159609;G:822435259;T:1023096853;N:103767,150,0,,,963212012,848159609,822435259,1023096853,103767,SRX5914453,SRS4832641,SRA891446,Kunming University of Science and Technology|College of Life Science,Kunming University of Science and Technology,1,0.92318,,0.03725,,0.72997,,0.48413,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-29,Adult,Adult,Gut,Digestive System
52342,SRR9141306,SRX5914452,SRS4832640,SRP199735,PRJNA545244,Zebrafish transcriptome data,PRJNA545244,Other,Heavy metals stimulate zebrafish,,,,,Drck1 aliquot,,isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female gut,Drck1,Drck1,Gene expression in zebrafish stimulated by heavy metals,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP199735,,,Drck1 (pooling35-ACTTGA_HY2FYCCXY_L8_1.fq and pooling35-ACTTGA_HY2FYCCXY_L8_2.fq).gz,fastq,3523656300.0,23491042.0,Drck1 pooling35 ACTTGA HY2FYCCXY L8 1.fq and pooling35 ACTTGA HY2FYCCXY L8 2.fq.gz,0:0 1:150,A:973145926;C:804077269;G:862830763;T:883447878;N:154464,0,150,,,973145926,804077269,862830763,883447878,154464,SRX5914452,SRS4832640,SRA891446,Kunming University of Science and Technology|College of Life Science,Kunming University of Science and Technology,1,0.93236,,0.03761,,0.7134,,0.49667,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-29,Adult,Adult,Gut,Digestive System
52343,SRR9141307,SRX5914451,SRS4832639,SRP199735,PRJNA545244,Zebrafish transcriptome data,PRJNA545244,Other,Heavy metals stimulate zebrafish,,,,,Drck2 aliquot,,isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female gut,Drck2,Drck2,Gene expression in zebrafish stimulated by heavy metals,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP199735,,,Drck2 (pooling35-GATCAG_HY2FYCCXY_L8_1.fq and pooling35-GATCAG_HY2FYCCXY_L8_2.fq).gz,fastq,3720733950.0,24804893.0,Drck2 pooling35 GATCAG HY2FYCCXY L8 1.fq and pooling35 GATCAG HY2FYCCXY L8 2.fq.gz,0:0 1:150,A:1041160797;C:830715515;G:904059203;T:944636106;N:162329,0,150,,,1041160797,830715515,904059203,944636106,162329,SRX5914451,SRS4832639,SRA891446,Kunming University of Science and Technology|College of Life Science,Kunming University of Science and Technology,1,0.91965,,0.0417,,0.70483,,0.48829,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-29,Adult,Adult,Gut,Digestive System
53594,SRR9960231,SRX6707776,SRS5261677,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs200vm,GSM4029395,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200μm PS MPs,MPs200vm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200μm PS MPs,GSM4029395,GSM4029395: MPs200vm; Danio rerio; RNA Seq,GSM4029395,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029395,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs200vm_1.fq.gz MPs200vm_2.fq.gz,fastq fastq,105309618900.0,351032063.0,GSM4029395 r1,0:150 1:150,A:27241602982;C:19773063887;G:28015499540;T:30277575281;N:1877210,150,150,,,27241602982,19773063887,28015499540,30277575281,1877210,SRX6707776,SRS5261677,SRA938912,GEO,Nanjing University,2,0.0,0.87735,0.0,0.07963,1.0,0.83049,,0.55138,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53595,SRR9960230,SRX6707775,SRS5261676,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs5vm,GSM4029394,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5μm PS MPs,MPs5vm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5μm PS MPs,GSM4029394,GSM4029394: MPs5vm; Danio rerio; RNA Seq,GSM4029394,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029394,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs5vm_1.fq.gz MPs5vm_2.fq.gz,fastq fastq,98563904100.0,328546347.0,GSM4029394 r1,0:150 1:150,A:26023907285;C:17974044830;G:25736568268;T:28827634883;N:1748834,150,150,,,26023907285,17974044830,25736568268,28827634883,1748834,SRX6707775,SRS5261676,SRA938912,GEO,Nanjing University,2,0.0,0.86592,0.0,0.09908,1.0,0.81552,,0.55476,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53596,SRR9960229,SRX6707774,SRS5261675,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs100nm,GSM4029393,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:100nm PS MPs,MPs100nm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:100nm PS MPs,GSM4029393,GSM4029393: MPs100nm; Danio rerio; RNA Seq,GSM4029393,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029393,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs100nm_1.fq.gz MPs100nm_2.fq.gz,fastq fastq,122539718400.0,408465728.0,GSM4029393 r1,0:150 1:150,A:32283417066;C:22576112318;G:30470461014;T:37207888685;N:1839317,150,150,,,32283417066,22576112318,30470461014,37207888685,1839317,SRX6707774,SRS5261675,SRA938912,GEO,Nanjing University,2,0.0,0.88187,0.0,0.09087,1.0,0.82428,,0.53597,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53597,SRR9960228,SRX6707773,SRS5261674,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,CK,GSM4029392,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:n1,CK,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:n1,GSM4029392,GSM4029392: CK; Danio rerio; RNA Seq,GSM4029392,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029392,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,CK_1.fq.gz CK_2.fq.gz,fastq fastq,111761141100.0,372537137.0,GSM4029392 r1,0:150 1:150,A:29264568248;C:21295511514;G:29897320083;T:31301732224;N:2009031,150,150,,,29264568248,21295511514,29897320083,31301732224,2009031,SRX6707773,SRS5261674,SRA938912,GEO,Nanjing University,2,0.0,0.88395,0.0,0.08593,1.0,0.80466,,0.46326,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
55951,SRR10827995,SRX7501389,SRS5942789,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR011,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate10|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR011,ZR011,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR011_S00_L009_R2_001.fastq.gz lane9-ZR011_S00_L009_R1_001.fastq.gz,fastq fastq,9665147298.0,32003799.0,lane9 ZR011 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2665223251;C:2186863125;G:2211599706;T:2600518585;N:942631,151,151,,,2665223251,2186863125,2211599706,2600518585,942631,SRX7501389,SRS5942789,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.85775,0.85388,0.06267,0.06297,0.78766,0.79097,0.54825,0.54162,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55952,SRR10827996,SRX7501388,SRS5942788,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR010,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate9|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR010,ZR010,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR010_S00_L009_R2_001.fastq.gz lane9-ZR010_S00_L009_R1_001.fastq.gz,fastq fastq,10313891618.0,34151959.0,lane9 ZR010 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2810497988;C:2363542718;G:2386667646;T:2752188319;N:994947,151,151,,,2810497988,2363542718,2386667646,2752188319,994947,SRX7501388,SRS5942788,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.86439,0.85421,0.05536,0.05624,0.78378,0.78847,0.5643,0.5428,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55953,SRR10827997,SRX7501387,SRS5942787,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR009,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate8|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR009,ZR009,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR009_S00_L009_R2_001.fastq.gz lane9-ZR009_S00_L009_R1_001.fastq.gz,fastq fastq,8998700946.0,29797023.0,lane9 ZR009 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2553315628;C:1959457429;G:1980318504;T:2504726656;N:882729,151,151,,,2553315628,1959457429,1980318504,2504726656,882729,SRX7501387,SRS5942787,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.80444,0.8015,0.08208,0.08274,0.78634,0.78813,0.56791,0.56822,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55954,SRR10827998,SRX7501386,SRS5942786,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR008,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate7|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR008,ZR008,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR008_S00_L009_R1_001.fastq.gz lane9-ZR008_S00_L009_R2_001.fastq.gz,fastq fastq,9206500200.0,30485100.0,lane9 ZR008 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2571733836;C:2048238935;G:2081481702;T:2504158985;N:886742,151,151,,,2571733836,2048238935,2081481702,2504158985,886742,SRX7501386,SRS5942786,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.84315,0.84243,0.06679,0.068,0.79026,0.79263,0.54865,0.52814,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55955,SRR10827999,SRX7501385,SRS5942785,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR006,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate6|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR006,ZR006,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR006_S00_L009_R1_001.fastq.gz lane9-ZR006_S00_L009_R2_001.fastq.gz,fastq fastq,9469616190.0,31356345.0,lane9 ZR006 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2598567090;C:2156360016;G:2166235031;T:2547531313;N:922740,151,151,,,2598567090,2156360016,2166235031,2547531313,922740,SRX7501385,SRS5942785,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.86997,0.86634,0.06206,0.06323,0.7853,0.7877,0.5039,0.48672,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55956,SRR10828000,SRX7501384,SRS5942783,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR005,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR005,ZR005,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR005_S00_L009_R1_001.fastq.gz lane9-ZR005_S00_L009_R2_001.fastq.gz,fastq fastq,8265125732.0,27367966.0,lane9 ZR005 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2271031367;C:1878130541;G:1893994523;T:2221168810;N:800491,151,151,,,2271031367,1878130541,1893994523,2221168810,800491,SRX7501384,SRS5942783,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.87646,0.7655,0.06913,0.06038,0.79401,0.80915,0.54875,0.54807,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55957,SRR10828001,SRX7501383,SRS5942784,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR004,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR004,ZR004,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR004_S00_L009_R1_001.fastq.gz lane9-ZR004_S00_L009_R2_001.fastq.gz,fastq fastq,9015407586.0,29852343.0,lane9 ZR004 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2508921769;C:2018051929;G:2030281337;T:2457279135;N:873416,151,151,,,2508921769,2018051929,2030281337,2457279135,873416,SRX7501383,SRS5942784,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.84988,0.83488,0.06628,0.06644,0.77344,0.77843,0.55247,0.5423,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55958,SRR10828002,SRX7501382,SRS5942782,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR022,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate21|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR022,ZR022,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR022_S00_L009_R1_001.fastq.gz lane9-ZR022_S00_L009_R2_001.fastq.gz,fastq fastq,13741876102.0,45502901.0,lane9 ZR022 S00 L009 R1 001.fastq.gz,0:151 1:151,A:3931077197;C:2931142966;G:2955027469;T:3923313652;N:1314818,151,151,,,3931077197,2931142966,2955027469,3923313652,1314818,SRX7501382,SRS5942782,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.88334,0.87862,0.09332,0.09391,0.77711,0.78113,0.55947,0.54508,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55959,SRR10828003,SRX7501381,SRS5942781,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR003,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR003,ZR003,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR003_S00_L009_R1_001.fastq.gz lane9-ZR003_S00_L009_R2_001.fastq.gz,fastq fastq,11201243420.0,37090210.0,lane9 ZR003 S00 L009 R1 001.fastq.gz,0:151 1:151,A:3127283035;C:2496207030;G:2513262555;T:3063404560;N:1086240,151,151,,,3127283035,2496207030,2513262555,3063404560,1086240,SRX7501381,SRS5942781,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.86792,0.8632,0.06784,0.06862,0.78867,0.79308,0.53988,0.52892,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55960,SRR10828004,SRX7501380,SRS5942780,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR021,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate20|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR021,ZR021,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR021_S00_L009_R1_001.fastq.gz lane9-ZR021_S00_L009_R2_001.fastq.gz,fastq fastq,10099985924.0,33443662.0,lane9 ZR021 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2774168141;C:2288982049;G:2309143011;T:2726709515;N:983208,151,151,,,2774168141,2288982049,2309143011,2726709515,983208,SRX7501380,SRS5942780,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.86982,0.86834,0.07188,0.07308,0.78717,0.78987,0.5574,0.5503,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55961,SRR10828005,SRX7501379,SRS5942779,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR020,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate19|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR020,ZR020,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR020_S00_L009_R1_001.fastq.gz lane9-ZR020_S00_L009_R2_001.fastq.gz,fastq fastq,10454972428.0,34619114.0,lane9 ZR020 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2839651351;C:2416116684;G:2429373737;T:2768795024;N:1035632,151,151,,,2839651351,2416116684,2429373737,2768795024,1035632,SRX7501379,SRS5942779,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.86093,0.86611,0.03397,0.03484,0.83104,0.83327,0.30434,0.30026,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55962,SRR10828006,SRX7501378,SRS5942778,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR019,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate18|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR019,ZR019,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR019_S00_L009_R2_001.fastq.gz lane9-ZR019_S00_L009_R1_001.fastq.gz,fastq fastq,10719453458.0,35494879.0,lane9 ZR019 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2914826334;C:2463706695;G:2484150600;T:2855735087;N:1034742,151,151,,,2914826334,2463706695,2484150600,2855735087,1034742,SRX7501378,SRS5942778,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.87668,0.87454,0.05478,0.05538,0.78884,0.7906,0.53897,0.5064,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55963,SRR10828007,SRX7501377,SRS5942777,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR018,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate17|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR018,ZR018,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR018_S00_L009_R1_001.fastq.gz lane9-ZR018_S00_L009_R2_001.fastq.gz,fastq fastq,6358250620.0,21053810.0,lane9 ZR018 S00 L009 R1 001.fastq.gz,0:151 1:151,A:1669813509;C:1524057927;G:1530947497;T:1632824279;N:607408,151,151,,,1669813509,1524057927,1530947497,1632824279,607408,SRX7501377,SRS5942777,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.89698,0.89547,0.05683,0.05916,0.81848,0.82089,0.56455,0.54732,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System
55964,SRR10828008,SRX7501376,SRS5942776,SRP239446,PRJNA598916,Zebrafish intestinal gene expression,PRJNA598916,Other,An analysis of zebrafish intestinal gene expression,,,,,ZR017,,strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate16|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult 5D intestine,ZR017,ZR017,Illumina Paired end sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP239446,,,lane9-ZR017_S00_L009_R1_001.fastq.gz lane9-ZR017_S00_L009_R2_001.fastq.gz,fastq fastq,8141425324.0,26958362.0,lane9 ZR017 S00 L009 R1 001.fastq.gz,0:151 1:151,A:2210048052;C:1874541787;G:1892972101;T:2163066000;N:797384,151,151,,,2210048052,1874541787,1892972101,2163066000,797384,SRX7501376,SRS5942776,SRA1020118,Oregon State University|Microbiology,Oregon State University,2,0.8799,0.75762,0.05488,0.04911,0.78587,0.80105,0.5506,0.52986,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-01-04,Adult,Adult,Gut,Digestive System