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 1500,1260Application ReadForward1,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 1500,1260Application ReadForward1,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 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529460,,,,3480523704.0,27623204.0,DRR408240,0:126 1:0,A:898051986;C:827557593;G:816541244;T:938307607;N:65274,126,0,,,898051986,827557593,816541244,938307607,65274,DRX393846,DRS407004,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Adult,Adult,Gut,Digestive System
35,DRR408239,DRX393845,DRS407003,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 3,zebrafish larval gut replicate 3,SAMD00529459,,sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529459,DRX393845,AR012 gut 5 5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529459,,,,3463982046.0,27491921.0,DRR408239,0:126 1:0,A:842552557;C:849757648;G:837664725;T:933942026;N:65090,126,0,,,842552557,849757648,837664725,933942026,65090,DRX393845,DRS407003,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
36,DRR408238,DRX393844,DRS407002,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 2,zebrafish larval gut replicate 2,SAMD00529458,,sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529458,DRX393844,AR005 gut 3 5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529458,,,,3782320416.0,30018416.0,DRR408238,0:126 1:0,A:930337206;C:920645770;G:906559955;T:1024704277;N:73208,126,0,,,930337206,920645770,906559955,1024704277,73208,DRX393844,DRS407002,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
37,DRR408237,DRX393843,DRS407001,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 1,zebrafish larval gut replicate 1,SAMD00529457,,sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529457,DRX393843,AR002 gut 1 5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,1260Application ReadForward1,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529457,,,,3606885828.0,28626078.0,DRR408237,0:126 1:0,A:879148446;C:885673723;G:870330963;T:971663212;N:69484,126,0,,,879148446,885673723,870330963,971663212,69484,DRX393843,DRS407001,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
172,DRR075398,DRX069312,DRS075493,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The gut of control fish 7dpf,Control gut,SAMD00065412,,sample name:2 control gut 150701 Hiseq3A l3 018|tissue type:Gut,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065412,DRX069312,Control gut,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,360Application ReadForward1,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065412,,,,1008093492.0,28002597.0,DRR075398,0:36,A:230431417;C:251640901;G:244174255;T:281811580;N:35339,36,,,,230431417,251640901,244174255,281811580,35339,DRX069312,DRS075493,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.9173,,0.07181,,0.72017,,0.45193,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Gut,Digestive System
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 4000,8660FApplication ReadForward11RApplication ReadReverse434,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 4000,8660FApplication ReadForward11RApplication ReadReverse434,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 4000,8660FApplication ReadForward11RApplication ReadReverse434,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 4000,8660FApplication ReadForward11RApplication ReadReverse434,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
24918,SRR25594442,SRX21322829,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,Z 2 1.fq,Z 2 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,Z-2_2.fq.gz Z-2_1.fq.gz,fastq fastq,5621492400.0,18738308.0,Z 2 1.fq.gz,0:150 1:150,A:1483421677;C:1306378425;G:1338052121;T:1493618330;N:21847,150,150,,,1483421677,1306378425,1338052121,1493618330,21847,SRX21322829,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94389,0.93819,0.03702,0.03621,0.71758,0.72423,0.43774,0.4558,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24919,SRR25594443,SRX21322828,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,Z 1 1.fq,Z 1 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,Z-1_2.fq.gz Z-1_1.fq.gz,fastq fastq,6301274700.0,21004249.0,Z 1 1.fq.gz,0:150 1:150,A:1671253253;C:1458678359;G:1491311308;T:1680006330;N:25450,150,150,,,1671253253,1458678359,1491311308,1680006330,25450,SRX21322828,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94339,0.93817,0.03831,0.03813,0.71752,0.72293,0.42611,0.43548,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24920,SRR25594444,SRX21322827,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,K 3 1.fq,K 3 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,K-3_2.fq.gz K-3_1.fq.gz,fastq fastq,5519682000.0,18398940.0,K 3 1.fq.gz,0:150 1:150,A:1469946965;C:1270791684;G:1304075220;T:1474846842;N:21289,150,150,,,1469946965,1270791684,1304075220,1474846842,21289,SRX21322827,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94356,0.93561,0.03986,0.03923,0.71877,0.72697,0.44771,0.44936,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24921,SRR25594445,SRX21322826,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,K 2 1.fq,K 2 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,K-2_1.fq.gz K-2_2.fq.gz,fastq fastq,5808261300.0,19360871.0,K 2 1.fq.gz,0:150 1:150,A:1538012312;C:1343217111;G:1375887577;T:1551118640;N:25660,150,150,,,1538012312,1343217111,1375887577,1551118640,25660,SRX21322826,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94469,0.94137,0.03929,0.03857,0.7175,0.71946,0.44395,0.44354,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24922,SRR25594446,SRX21322825,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,ZP 3 1.fq,ZP 3 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,ZP-3_1.fq.gz ZP-3_2.fq.gz,fastq fastq,5397938100.0,17993127.0,ZP 3 1.fq.gz,0:150 1:150,A:1438191584;C:1244532731;G:1271700792;T:1443491138;N:21855,150,150,,,1438191584,1244532731,1271700792,1443491138,21855,SRX21322825,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94839,0.94406,0.04345,0.04279,0.71719,0.72362,0.42772,0.4311,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24923,SRR25594447,SRX21322824,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,ZP 2 1.fq,ZP 2 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,ZP-2_1.fq.gz ZP-2_2.fq.gz,fastq fastq,6062424900.0,20208083.0,ZP 2 1.fq.gz,0:150 1:150,A:1612595576;C:1398589726;G:1427536119;T:1623678727;N:24752,150,150,,,1612595576,1398589726,1427536119,1623678727,24752,SRX21322824,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.95013,0.94657,0.04364,0.04342,0.71565,0.71908,0.44652,0.44832,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24924,SRR25594448,SRX21322823,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,ZP 1 1.fq,ZP 1 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,ZP-1_2.fq.gz ZP-1_1.fq.gz,fastq fastq,6487607100.0,21625357.0,ZP 1 1.fq.gz,0:150 1:150,A:1728514584;C:1494175744;G:1521726756;T:1743164500;N:25516,150,150,,,1728514584,1494175744,1521726756,1743164500,25516,SRX21322823,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94867,0.94432,0.04535,0.0449,0.71926,0.72348,0.43747,0.44661,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24925,SRR25594449,SRX21322822,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,Z 3 1.fq,Z 3 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,Z-3_1.fq.gz Z-3_2.fq.gz,fastq fastq,8111204700.0,27037349.0,Z 3 1.fq.gz,0:150 1:150,A:2143712842;C:1879826122;G:1918517283;T:2169119328;N:29125,150,150,,,2143712842,1879826122,1918517283,2169119328,29125,SRX21322822,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94485,0.94083,0.03886,0.03798,0.71362,0.71768,0.44066,0.44713,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
24926,SRR25594450,SRX21322821,SRS18569855,SRP454395,PRJNA1002816,Danio rerio Raw sequence reads,PRJNA1002816,Whole Genome Sequencing,Zebrafish Transcriptome,,,,,Zebrafish intestine,,strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Intestinal Transcriptome,K 1 1.fq,K 1 1.fq,Intestinal Transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454395,,,K-1_1.fq.gz K-1_2.fq.gz,fastq fastq,7164142200.0,23880474.0,K 1 1.fq.gz,0:150 1:150,A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789,150,150,,,1896647470,1661542391,1700422400,1905500150,29789,SRX21322821,SRS18569855,SRA1689922,"Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish","Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences",2,0.94635,0.94209,0.03738,0.03664,0.71961,0.72571,0.45014,0.44857,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-10,Undetermined,Undetermined,Gut,Digestive System
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
29041,SRR26990794,SRX22683825,SRS19677539,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut3,GSM7924158,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924158,GSM7924158: WT gut3; Danio rerio; RNA Seq,GSM7924158 r1,GSM7924158,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz,fastq fastq,6066709786.0,20088443.0,GSM7924158 r1,0:151 1:151,A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156,151,151,,,1673762656,1360901090,1385125931,1646863953,56156,SRX22683825,SRS19677539,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.92515,0.9297,0.0691,0.0659,0.75041,0.75022,0.53007,0.53064,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29042,SRR26990795,SRX22683824,SRS19677538,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut2,GSM7924157,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924157,GSM7924157: WT gut2; Danio rerio; RNA Seq,GSM7924157 r1,GSM7924157,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz,fastq fastq,5406867570.0,17903535.0,GSM7924157 r1,0:151 1:151,A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612,151,151,,,1464846243,1237183908,1259215309,1445572498,49612,SRX22683824,SRS19677538,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93795,0.94322,0.05952,0.05592,0.75933,0.75887,0.54179,0.53451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29043,SRR26990796,SRX22683823,SRS19677537,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut1,GSM7924156,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924156,GSM7924156: WT gut1; Danio rerio; RNA Seq,GSM7924156 r1,GSM7924156,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz,fastq fastq,5162192908.0,17093354.0,GSM7924156 r1,0:151 1:151,A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343,151,151,,,1404682153,1175657030,1196829496,1384975886,48343,SRX22683823,SRS19677537,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93119,0.93585,0.06122,0.05809,0.74757,0.74757,0.54124,0.54417,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29044,SRR26990797,SRX22683822,SRS19677536,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut3,GSM7924155,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924155,GSM7924155: itgavKO gut3; Danio rerio; RNA Seq,GSM7924155 r1,GSM7924155,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz,fastq fastq,4146743578.0,13730939.0,GSM7924155 r1,0:151 1:151,A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387,151,151,,,1130002132,943522869,958031732,1115146458,40387,SRX22683822,SRS19677536,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93764,0.94144,0.05938,0.05594,0.7553,0.75485,0.55535,0.55018,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29045,SRR26990798,SRX22683821,SRS19677535,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut2,GSM7924154,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924154,GSM7924154: itgavKO gut2; Danio rerio; RNA Seq,GSM7924154 r1,GSM7924154,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz,fastq fastq,4225756140.0,13992570.0,GSM7924154 r1,0:151 1:151,A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530,151,151,,,1133211420,974497998,995876972,1122129220,40530,SRX22683821,SRS19677535,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.95341,0.95884,0.05109,0.04883,0.77542,0.77368,0.51301,0.50704,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29046,SRR26990799,SRX22683820,SRS19677534,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itagvKO gut1,GSM7924153,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itagvKO gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924153,GSM7924153: itagvKO gut1; Danio rerio; RNA Seq,GSM7924153 r1,GSM7924153,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz,fastq fastq,5954117844.0,19715622.0,GSM7924153 r1,0:151 1:151,A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859,151,151,,,1600496071,1372939932,1393534700,1587094282,52859,SRX22683820,SRS19677534,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.94807,0.95298,0.05682,0.05385,0.74004,0.73925,0.54423,0.54484,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29575,SRR27387418,SRX23063709,SRS20023731,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 6,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate6|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 6,T8 6,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A54_1.fastq.gz A54_2.fastq.gz,fastq fastq,8459790000.0,28199300.0,A54 1.fastq.gz,0:150 1:150,A:2287135948;C:1957145280;G:1959338891;T:2256075943;N:93938,150,150,,,2287135948,1957145280,1959338891,2256075943,93938,SRX23063709,SRS20023731,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92583,0.92422,0.06345,0.06263,0.75718,0.75757,0.52145,0.5361,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29576,SRR27387419,SRX23063708,SRS20023730,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 5,T8 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A53_1.fastq.gz A53_2.fastq.gz,fastq fastq,8302022700.0,27673409.0,A53 1.fastq.gz,0:150 1:150,A:2241277601;C:1925048164;G:1920142999;T:2215462687;N:91249,150,150,,,2241277601,1925048164,1920142999,2215462687,91249,SRX23063708,SRS20023730,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92711,0.92566,0.06314,0.06353,0.75221,0.75219,0.541,0.53579,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29577,SRR27387420,SRX23063707,SRS20023729,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 4,T8 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A49_1.fastq.gz A49_2.fastq.gz,fastq fastq,6939976800.0,23133256.0,A49 1.fastq.gz,0:150 1:150,A:1895013575;C:1589528661;G:1585890890;T:1869466351;N:77323,150,150,,,1895013575,1589528661,1585890890,1869466351,77323,SRX23063707,SRS20023729,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92632,0.92542,0.06323,0.06265,0.75588,0.75722,0.55002,0.55324,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29578,SRR27387421,SRX23063706,SRS20023728,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 3,T8 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A44_1.fastq.gz A44_2.fastq.gz,fastq fastq,9116379900.0,30387933.0,A44 1.fastq.gz,0:150 1:150,A:2462347514;C:2113718621;G:2112401730;T:2427812186;N:99849,150,150,,,2462347514,2113718621,2112401730,2427812186,99849,SRX23063706,SRS20023728,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93154,0.92882,0.06321,0.06277,0.75499,0.75519,0.54224,0.542,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29579,SRR27387422,SRX23063705,SRS20023727,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 2,T8 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A43_1.fastq.gz A43_2.fastq.gz,fastq fastq,7681997100.0,25606657.0,A43 1.fastq.gz,0:150 1:150,A:2098281007;C:1758609887;G:1757658923;T:2067364339;N:82944,150,150,,,2098281007,1758609887,1757658923,2067364339,82944,SRX23063705,SRS20023727,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92257,0.92131,0.07154,0.07125,0.74769,0.74712,0.52352,0.51843,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29580,SRR27387423,SRX23063704,SRS20023726,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Combined Intestine,combined intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T8 1,T8 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A29_1.fastq.gz A29_2.fastq.gz,fastq fastq,8869294500.0,29564315.0,A29 1.fastq.gz,0:150 1:150,A:2411657291;C:2043119196;G:2038118093;T:2376336869;N:63051,150,150,,,2411657291,2043119196,2038118093,2376336869,63051,SRX23063704,SRS20023726,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.9293,0.93157,0.06846,0.06859,0.75138,0.75209,0.54348,0.54178,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29582,SRR27387425,SRX23063702,SRS20023724,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 5,T7 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A51_1.fastq.gz A51_2.fastq.gz,fastq fastq,8229865500.0,27432885.0,A51 1.fastq.gz,0:150 1:150,A:2239224965;C:1891494000;G:1890511233;T:2208544358;N:90944,150,150,,,2239224965,1891494000,1890511233,2208544358,90944,SRX23063702,SRS20023724,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.9282,0.92676,0.06786,0.06815,0.74566,0.74673,0.54961,0.55067,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29583,SRR27387426,SRX23063701,SRS20023723,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 4,T7 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A50_1.fastq.gz A50_2.fastq.gz,fastq fastq,8549274300.0,28497581.0,A50 1.fastq.gz,0:150 1:150,A:2321938070;C:1971518879;G:1967040023;T:2288683614;N:93714,150,150,,,2321938070,1971518879,1967040023,2288683614,93714,SRX23063701,SRS20023723,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93231,0.93126,0.06361,0.06304,0.7527,0.75211,0.48289,0.48336,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29584,SRR27387427,SRX23063700,SRS20023722,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 3,T7 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A48_1.fastq.gz A48_2.fastq.gz,fastq fastq,8065026000.0,26883420.0,A48 1.fastq.gz,0:150 1:150,A:2177870889;C:1870003683;G:1870725132;T:2146337507;N:88789,150,150,,,2177870889,1870003683,1870725132,2146337507,88789,SRX23063700,SRS20023722,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92891,0.92753,0.05842,0.05778,0.71991,0.72009,0.51653,0.51675,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29585,SRR27387428,SRX23063699,SRS20023721,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 2,T7 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A42_1.fastq.gz A42_2.fastq.gz,fastq fastq,8391356700.0,27971189.0,A42 1.fastq.gz,0:150 1:150,A:2247673277;C:1962692430;G:1966871884;T:2214026582;N:92527,150,150,,,2247673277,1962692430,1966871884,2214026582,92527,SRX23063699,SRS20023721,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93153,0.93045,0.05902,0.05934,0.75424,0.75546,0.548,0.54354,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29586,SRR27387429,SRX23063698,SRS20023720,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Nanoplastics Intestine,nps intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T7 1,T7 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A31_1.fastq.gz A31_2.fastq.gz,fastq fastq,8236557000.0,27455190.0,A31 1.fastq.gz,0:150 1:150,A:2204148101;C:1929010419;G:1925723147;T:2177582914;N:92419,150,150,,,2204148101,1929010419,1925723147,2177582914,92419,SRX23063698,SRS20023720,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93739,0.93581,0.06216,0.06176,0.75057,0.75049,0.54176,0.53414,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29587,SRR27387430,SRX23063697,SRS20023719,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 6,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate6|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 6,T6 6,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A56_1.fastq.gz A56_2.fastq.gz,fastq fastq,6435464400.0,21451548.0,A56 1.fastq.gz,0:150 1:150,A:1748400934;C:1486171533;G:1481023797;T:1719795546;N:72590,150,150,,,1748400934,1486171533,1481023797,1719795546,72590,SRX23063697,SRS20023719,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92722,0.92559,0.0729,0.07288,0.74288,0.74343,0.53587,0.52589,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29588,SRR27387431,SRX23063696,SRS20023718,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 5,T6 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A40_1.fastq.gz A40_2.fastq.gz,fastq fastq,8749914000.0,29166380.0,A40 1.fastq.gz,0:150 1:150,A:2338416402;C:2051360445;G:2055480569;T:2304561447;N:95137,150,150,,,2338416402,2051360445,2055480569,2304561447,95137,SRX23063696,SRS20023718,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.94523,0.9504,0.03896,0.03887,0.80661,0.80728,0.46402,0.45996,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29589,SRR27387432,SRX23063695,SRS20023717,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 4,T6 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A39_1.fastq.gz A39_2.fastq.gz,fastq fastq,8140938300.0,27136461.0,A39 1.fastq.gz,0:150 1:150,A:2198617601;C:1888830697;G:1887283102;T:2166117857;N:89043,150,150,,,2198617601,1888830697,1887283102,2166117857,89043,SRX23063695,SRS20023717,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92636,0.92532,0.05883,0.0588,0.71689,0.71593,0.52397,0.5214,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29590,SRR27387433,SRX23063694,SRS20023716,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 3,T6 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A35_1.fastq.gz A35_2.fastq.gz,fastq fastq,6912319200.0,23041064.0,A35 1.fastq.gz,0:150 1:150,A:1895216825;C:1576630157;G:1574441195;T:1865953455;N:77568,150,150,,,1895216825,1576630157,1574441195,1865953455,77568,SRX23063694,SRS20023716,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92983,0.92816,0.072,0.07173,0.76601,0.76615,0.55997,0.55562,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29591,SRR27387434,SRX23063693,SRS20023715,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 2,T6 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A34_1.fastq.gz A34_2.fastq.gz,fastq fastq,7279802100.0,24266007.0,A34 1.fastq.gz,0:150 1:150,A:1989158951;C:1663891494;G:1668311413;T:1958359476;N:80766,150,150,,,1989158951,1663891494,1668311413,1958359476,80766,SRX23063693,SRS20023715,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92923,0.92655,0.06821,0.068,0.74042,0.74128,0.54366,0.54276,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29593,SRR27387436,SRX23063691,SRS20023713,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,6PPDQ Intestine,6ppdq intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T6 1,T6 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A30_1.fastq.gz A30_2.fastq.gz,fastq fastq,7219947600.0,24066492.0,A30 1.fastq.gz,0:150 1:150,A:1901354175;C:1717600917;G:1716606554;T:1884305293;N:80661,150,150,,,1901354175,1717600917,1716606554,1884305293,80661,SRX23063691,SRS20023713,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93375,0.93214,0.05513,0.05567,0.74759,0.74698,0.5475,0.54855,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29594,SRR27387437,SRX23063690,SRS20023712,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 6,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate6|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 6,T5 6,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A46_1.fastq.gz A46_2.fastq.gz,fastq fastq,8509361100.0,28364537.0,A46 1.fastq.gz,0:150 1:150,A:2341600956;C:1932495972;G:1930461855;T:2304710926;N:91391,150,150,,,2341600956,1932495972,1930461855,2304710926,91391,SRX23063690,SRS20023712,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92542,0.92408,0.07033,0.06986,0.77234,0.77199,0.55246,0.55942,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29595,SRR27387438,SRX23063689,SRS20023711,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 5,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate5|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 5,T5 5,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A45_1.fastq.gz A45_2.fastq.gz,fastq fastq,7856294100.0,26187647.0,A45 1.fastq.gz,0:150 1:150,A:2129077180;C:1813666476;G:1813868805;T:2099595491;N:86148,150,150,,,2129077180,1813666476,1813868805,2099595491,86148,SRX23063689,SRS20023711,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93087,0.92866,0.06398,0.06358,0.75481,0.75597,0.55424,0.55289,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29596,SRR27387439,SRX23063688,SRS20023710,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 4,T5 4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A38_1.fastq.gz A38_2.fastq.gz,fastq fastq,8039208600.0,26797362.0,A38 1.fastq.gz,0:150 1:150,A:2201215819;C:1836215616;G:1833348507;T:2168337651;N:91007,150,150,,,2201215819,1836215616,1833348507,2168337651,91007,SRX23063688,SRS20023710,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.9219,0.91957,0.0702,0.06947,0.76343,0.76493,0.55355,0.54863,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29597,SRR27387440,SRX23063687,SRS20023709,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 3,T5 3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A37_1.fastq.gz A37_2.fastq.gz,fastq fastq,8253642600.0,27512142.0,A37 1.fastq.gz,0:150 1:150,A:2254958000;C:1889478281;G:1886099650;T:2223014303;N:92366,150,150,,,2254958000,1889478281,1886099650,2223014303,92366,SRX23063687,SRS20023709,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92632,0.92477,0.06268,0.06279,0.76719,0.76682,0.53773,0.53566,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29598,SRR27387441,SRX23063686,SRS20023708,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 2,T5 2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A33_1.fastq.gz A33_2.fastq.gz,fastq fastq,8276959500.0,27589865.0,A33 1.fastq.gz,0:150 1:150,A:2244800716;C:1909951370;G:1909130637;T:2212988991;N:87786,150,150,,,2244800716,1909951370,1909130637,2212988991,87786,SRX23063686,SRS20023708,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.93248,0.93089,0.06402,0.06475,0.701,0.7012,0.53585,0.53722,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
29599,SRR27387442,SRX23063685,SRS20023707,SRP480720,PRJNA1059246,Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish,PRJNA1059246,Other,Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.,,,,Control Intestine,control intestine 1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,T5 1,T5 1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP480720,,,A32_1.fastq.gz A32_2.fastq.gz,fastq fastq,7955418900.0,26518063.0,A32 1.fastq.gz,0:150 1:150,A:2236485440;C:1768380410;G:1765867470;T:2184596828;N:88752,150,150,,,2236485440,1768380410,1765867470,2184596828,88752,SRX23063685,SRS20023707,SRA1777576,Nord University|Faculty of Biosciences and Aquaculture,Nord University,2,0.92662,0.92301,0.071,0.07061,0.75207,0.75158,0.53095,0.54507,150,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2023-12-30,Adult,Adult,Gut,Digestive System
30620,SRR27907608,SRX23567386,SRS20412878,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,KO12. Ctla 4 knockout,GSM8068839,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO12. Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068839,GSM8068839: KO12. Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068839 r1,GSM8068839,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO12_Clean_Data2.fq.gz KO12_Clean_Data1.fq.gz,fastq fastq,5415971621.0,18199812.0,GSM8068839 r1,0:148.79 1:148.79,A:1482389043;C:1213758088;G:1232295642;T:1487496355;N:32493,148,148,,,1482389043,1213758088,1232295642,1487496355,32493,SRX23567386,SRS20412878,SRA1799527,zhejiang university,zhejiang university,2,0.86496,0.86584,0.08493,0.08156,0.73553,0.73588,0.50941,0.5104,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30621,SRR27907609,SRX23567385,SRS20412877,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,KO11 Ctla 4 knockout,GSM8068838,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO11 Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068838,GSM8068838: KO11 Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068838 r1,GSM8068838,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO11_Clean_Data2.fq.gz KO11_Clean_Data1.fq.gz,fastq fastq,5443694370.0,18290488.0,GSM8068838 r1,0:148.81 1:148.81,A:1480267395;C:1230300897;G:1247791644;T:1485302181;N:32253,148,148,,,1480267395,1230300897,1247791644,1485302181,32253,SRX23567385,SRS20412877,SRA1799527,zhejiang university,zhejiang university,2,0.86445,0.86409,0.07094,0.06652,0.74738,0.74897,0.51339,0.51762,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30622,SRR27907610,SRX23567384,SRS20412876,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,KO9 Ctla 4 knockout,GSM8068837,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO9 Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068837,GSM8068837: KO9 Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068837 r1,GSM8068837,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO9_Clean_Data2.fq.gz KO9_Clean_Data1.fq.gz,fastq fastq,5971590749.0,20072217.0,GSM8068837 r1,0:148.76 1:148.75,A:1640322573;C:1334570646;G:1352953128;T:1643708463;N:35939,148,148,,,1640322573,1334570646,1352953128,1643708463,35939,SRX23567384,SRS20412876,SRA1799527,zhejiang university,zhejiang university,2,0.86793,0.86937,0.07855,0.07588,0.74393,0.74523,0.50694,0.51104,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30623,SRR27907611,SRX23567383,SRS20412875,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,WT8 control,GSM8068836,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT8 control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068836,GSM8068836: WT8 control; Danio rerio; RNA Seq,GSM8068836 r1,GSM8068836,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT8_Clean_Data1.fq.gz WT8_Clean_Data2.fq.gz,fastq fastq,5740688401.0,19287992.0,GSM8068836 r1,0:148.82 1:148.81,A:1586419463;C:1274440057;G:1291660517;T:1588132746;N:35618,148,148,,,1586419463,1274440057,1291660517,1588132746,35618,SRX23567383,SRS20412875,SRA1799527,zhejiang university,zhejiang university,2,0.85516,0.85653,0.07987,0.07551,0.74515,0.74497,0.52575,0.52057,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30624,SRR27907612,SRX23567382,SRS20412874,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,WT7 control,GSM8068835,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT7 control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068835,GSM8068835: WT7 control; Danio rerio; RNA Seq,GSM8068835 r1,GSM8068835,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT7_Clean_Data2.fq.gz WT7_Clean_Data1.fq.gz,fastq fastq,5810188177.0,19521216.0,GSM8068835 r1,0:148.82 1:148.81,A:1609284873;C:1285068093;G:1302652710;T:1613147856;N:34645,148,148,,,1609284873,1285068093,1302652710,1613147856,34645,SRX23567382,SRS20412874,SRA1799527,zhejiang university,zhejiang university,2,0.83558,0.83684,0.08427,0.08011,0.75741,0.75836,0.52403,0.52405,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30625,SRR27907613,SRX23567381,SRS20412873,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,WT1 control,GSM8068834,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT1 control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068834,GSM8068834: WT1 control; Danio rerio; RNA Seq,GSM8068834 r1,GSM8068834,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT1_Clean_Data2.fq.gz WT1_Clean_Data1.fq.gz,fastq fastq,5771161671.0,19396834.0,GSM8068834 r1,0:148.77 1:148.76,A:1593780869;C:1284499295;G:1300298518;T:1592548515;N:34474,148,148,,,1593780869,1284499295,1300298518,1592548515,34474,SRX23567381,SRS20412873,SRA1799527,zhejiang university,zhejiang university,2,0.85731,0.85944,0.0704,0.06703,0.76601,0.76607,0.53065,0.53445,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30626,SRR27907720,SRX23567476,SRS20412967,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,KO scRNAseq,GSM8068833,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO scRNAseq,The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068833,GSM8068833: KO scRNAseq; Danio rerio; RNA Seq,GSM8068833 r1,GSM8068833,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,KO_S1_L001_R2_001.fastq.gz KO_S1_L001_R1_001.fastq.gz,fastq fastq,40958285011.0,344187269.0,GSM8068833 r1,0:28 1:91,A:11614416767;C:9247684357;G:9480911439;T:10614469263;N:803185,28,91,,,11614416767,9247684357,9480911439,10614469263,803185,SRX23567476,SRS20412967,SRA1799569,zhejiang university,zhejiang university,2,0.00982,0.9431,0.00356,0.10625,0.99277,0.8187,0.41297,0.63838,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30627,SRR27907721,SRX23567475,SRS20412966,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,WT scRNAseq,GSM8068832,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT scRNAseq,The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068832,GSM8068832: WT scRNAseq; Danio rerio; RNA Seq,GSM8068832 r1,GSM8068832,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz,fastq fastq,36724066995.0,308605605.0,GSM8068832 r1,0:28 1:91,A:10425178276;C:8399183780;G:8411777361;T:9487202777;N:724801,28,91,,,10425178276,8399183780,8411777361,9487202777,724801,SRX23567475,SRS20412966,SRA1799569,zhejiang university,zhejiang university,2,0.01141,0.94944,0.0039,0.1092,0.99324,0.841,0.43558,0.73314,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30694,SRR28272066,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775 HuNoV infected replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775 HuNoV infected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz,fastq fastq,6487168261.0,54514019.0,GSM8136771 r1,0:28 1:91,A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286,28,91,,,1754199332,1533792234,1687916105,1511168304,92286,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30695,SRR28272067,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775 HuNoV infected replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775 HuNoV infected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz,fastq fastq,6313572727.0,53055233.0,GSM8136771 r2,0:28 1:91,A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282,28,91,,,1709609257,1491468410,1640296277,1472111501,87282,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30696,SRR28272068,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774 HuNoV infected replicate 1 scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774 HuNoV infected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz,fastq fastq,15738518978.0,132256462.0,GSM8136770 r1,0:28 1:91,A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212,28,91,,,4181691582,3761213961,4083789142,3711597081,227212,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30697,SRR28272069,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774 HuNoV infected replicate 1 scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774 HuNoV infected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz,fastq fastq,15261653253.0,128249187.0,GSM8136770 r2,0:28 1:91,A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693,28,91,,,4059552936,3644406570,3954261902,3603216152,215693,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30698,SRR28272070,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773 uninfected replicate 2 scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773 uninfected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz,fastq fastq,15150656598.0,127316442.0,GSM8136769 r1,0:28 1:91,A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113,28,91,,,4100783574,3526779401,3845684506,3677189004,220113,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30699,SRR28272071,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773 uninfected replicate 2 scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773 uninfected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz,fastq fastq,14942015326.0,125563154.0,GSM8136769 r2,0:28 1:91,A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808,28,91,,,4048600218,3475105088,3787275869,3630822343,211808,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30700,SRR28272072,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772 uninfected replicate 1 scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772 uninfected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz,fastq fastq,7397061301.0,62160179.0,GSM8136768 r1,0:28 1:91,A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806,28,91,,,2023651844,1711760729,1860691426,1800850496,106806,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30701,SRR28272073,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772 uninfected replicate 1 scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772 uninfected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz,fastq fastq,7290496444.0,61264676.0,GSM8136768 r2,0:28 1:91,A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196,28,91,,,1996736343,1685693360,1830823892,1777138653,104196,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,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
33014,SRR29633212,SRX25139207,SRS21831220,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Mtz 5dpf,GSM8366963,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz 5dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366963,GSM8366963: Mtz 5dpf; Danio rerio; RNA Seq,GSM8366963 r1,GSM8366963,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Mtz-d5_R1.fastq.gz NTR-Mtz-d5_R2.fastq.gz,fastq fastq,105173263361.0,348971465.0,GSM8366963 r1,0:150.76 1:150.62,A:29260313483;C:18342577741;G:20471735616;T:37097033318;N:1603203,150,150,,,29260313483,18342577741,20471735616,37097033318,1603203,SRX25139207,SRS21831220,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.56019,0.89517,0.13273,0.11945,0.9795,0.82258,0.63676,0.6161,151,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33015,SRR29633213,SRX25139206,SRS21831219,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Control 5dpf,GSM8366962,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control 5dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366962,GSM8366962: Control 5dpf; Danio rerio; RNA Seq,GSM8366962 r1,GSM8366962,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Control-d5_R1.fastq.gz NTR-Control-d5_R2.fastq.gz,fastq fastq,139967773505.0,464402100.0,GSM8366962 r1,0:150.76 1:150.63,A:39202616731;C:24289494719;G:27175225437;T:49298534102;N:1902516,150,150,,,39202616731,24289494719,27175225437,49298534102,1902516,SRX25139206,SRS21831219,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.54902,0.89315,0.13449,0.13341,0.97954,0.80553,0.69256,0.59244,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33016,SRR29633214,SRX25139205,SRS21831218,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Mtz ablation 4dpf,GSM8366961,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz ablation 4dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366961,GSM8366961: Mtz ablation 4dpf; Danio rerio; RNA Seq,GSM8366961 r1,GSM8366961,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options: readTypes=BBTT read1PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R1 001.fastq.gz read2PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R2 001.fastq.gz read3PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I1 001.fastq.gz read4PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I2 001.fastq.gz,Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R1_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I1_001.fastq.gz,fastq fastq fastq fastq,33049837760.0,103280743.0,GSM8366961 r1,0:150 1:150 2:10 3:10,A:9739096160;C:6338831532;G:6106096444;T:8799858219;N:340545,150,150,10,10,9739096160,6338831532,6106096444,8799858219,340545,SRX25139205,SRS21831218,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.0,0.91169,0.0,0.19328,1.0,0.81722,,0.64993,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33017,SRR29633215,SRX25139204,SRS21831217,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Control ablation 4dpf,GSM8366960,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control ablation 4dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366960,GSM8366960: Control ablation 4dpf; Danio rerio; RNA Seq,GSM8366960 r1,GSM8366960,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options: readTypes=BBTT read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz,Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz,fastq fastq fastq fastq,115286504000.0,360270325.0,GSM8366960 r1,0:150 1:150 2:10 3:10,A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542,150,150,10,10,32679027944,17748865933,17885040590,39764959491,3203542,SRX25139204,SRS21831217,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.39015,0.90036,0.10989,0.19421,0.97845,0.79401,0.69547,0.6103,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33351,SRR30125634,SRX25595192,SRS22245033,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 3,GSM8439539,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439539,GSM8439539: SBM1 3; Danio rerio; RNA Seq,GSM8439539 r1,GSM8439539,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-3.R1.fq.gz SBM1-3.R2.fq.gz,fastq fastq,6920938402.0,24030624.0,GSM8439539 r1,0:144.00 1:144.00,A:1848518187;C:1602695225;G:1609135376;T:1860572175;N:17439,144,144,,,1848518187,1602695225,1609135376,1860572175,17439,SRX25595192,SRS22245033,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33352,SRR30125635,SRX25595191,SRS22245032,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 2,GSM8439538,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439538,GSM8439538: SBM1 2; Danio rerio; RNA Seq,GSM8439538 r1,GSM8439538,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-2.R1.fq.gz SBM1-2.R2.fq.gz,fastq fastq,6873386097.0,23812133.0,GSM8439538 r1,0:144.32 1:144.33,A:1794801562;C:1631426136;G:1638460090;T:1808681001;N:17308,144,144,,,1794801562,1631426136,1638460090,1808681001,17308,SRX25595191,SRS22245032,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33353,SRR30125636,SRX25595190,SRS22245031,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 1,GSM8439537,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439537,GSM8439537: SBM1 1; Danio rerio; RNA Seq,GSM8439537 r1,GSM8439537,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-1.R1.fq.gz SBM1-1.R2.fq.gz,fastq fastq,6893638362.0,23881631.0,GSM8439537 r1,0:144.33 1:144.33,A:1801507713;C:1634518350;G:1642455999;T:1815139080;N:17220,144,144,,,1801507713,1634518350,1642455999,1815139080,17220,SRX25595190,SRS22245031,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33354,SRR30125637,SRX25595189,SRS22245030,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 3,GSM8439536,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439536,GSM8439536: FM1 3; Danio rerio; RNA Seq,GSM8439536 r1,GSM8439536,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-3.R1.fq.gz FM1-3.R2.fq.gz,fastq fastq,6926890624.0,24044310.0,GSM8439536 r1,0:144.04 1:144.05,A:1814868011;C:1638590076;G:1645410775;T:1828004537;N:17225,144,144,,,1814868011,1638590076,1645410775,1828004537,17225,SRX25595189,SRS22245030,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33355,SRR30125638,SRX25595188,SRS22245029,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 2,GSM8439535,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439535,GSM8439535: FM1 2; Danio rerio; RNA Seq,GSM8439535 r1,GSM8439535,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-2.R1.fq.gz FM1-2.R2.fq.gz,fastq fastq,6932329149.0,24050700.0,GSM8439535 r1,0:144.12 1:144.12,A:1821635965;C:1634568957;G:1641356498;T:1834750114;N:17615,144,144,,,1821635965,1634568957,1641356498,1834750114,17615,SRX25595188,SRS22245029,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33356,SRR30125639,SRX25595187,SRS22245028,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 1,GSM8439534,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439534,GSM8439534: FM1 1; Danio rerio; RNA Seq,GSM8439534 r1,GSM8439534,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-1.R1.fq.gz FM1-1.R2.fq.gz,fastq fastq,6915521492.0,24044109.0,GSM8439534 r1,0:143.81 1:143.81,A:1851629842;C:1595942468;G:1602547587;T:1865384194;N:17401,143,143,,,1851629842,1595942468,1602547587,1865384194,17401,SRX25595187,SRS22245028,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33357,SRR30125640,SRX25595186,SRS22245027,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 3,GSM8439533,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439533,GSM8439533: D3 4 3; Danio rerio; RNA Seq,GSM8439533 r1,GSM8439533,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-3.R1.fq.gz D3-4-3.R2.fq.gz,fastq fastq,6934859246.0,24095045.0,GSM8439533 r1,0:143.91 1:143.91,A:1815846879;C:1641161510;G:1648091770;T:1829741658;N:17429,143,143,,,1815846879,1641161510,1648091770,1829741658,17429,SRX25595186,SRS22245027,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33358,SRR30125641,SRX25595185,SRS22245026,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 2,GSM8439532,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439532,GSM8439532: D3 4 2; Danio rerio; RNA Seq,GSM8439532 r1,GSM8439532,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-2.R1.fq.gz D3-4-2.R2.fq.gz,fastq fastq,7053487385.0,24519028.0,GSM8439532 r1,0:143.83 1:143.84,A:1888591272;C:1630003556;G:1636509489;T:1898365125;N:17943,143,143,,,1888591272,1630003556,1636509489,1898365125,17943,SRX25595185,SRS22245026,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33359,SRR30125642,SRX25595184,SRS22245025,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 1,GSM8439531,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439531,GSM8439531: D3 4 1; Danio rerio; RNA Seq,GSM8439531 r1,GSM8439531,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz,fastq fastq,6996797279.0,24229469.0,GSM8439531 r1,0:144.38 1:144.39,A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723,144,144,,,1841905352,1647600285,1654313322,1852960597,17723,SRX25595184,SRS22245025,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33417,SRR30186672,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L005_I1_001.fastq.gz FT-SA26637_S5_L005_R1_001.fastq.gz FT-SA26637_S5_L005_R2_001.fastq.gz,fastq fastq fastq,40502433410.0,130653011.0,GSM8448586 r1,0:8 1:151 2:151,A:10014178947;C:5704376875;G:6596271508;T:17137143949;N:5238043,8,151,151,,10014178947,5704376875,6596271508,17137143949,5238043,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33418,SRR30186673,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L006_I1_001.fastq.gz FT-SA26637_S5_L006_R1_001.fastq.gz FT-SA26637_S5_L006_R2_001.fastq.gz,fastq fastq fastq,41972742020.0,135395942.0,GSM8448586 r2,0:8 1:151 2:151,A:10346550415;C:6105559893;G:6757897068;T:17672755179;N:6811929,8,151,151,,10346550415,6105559893,6757897068,17672755179,6811929,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33419,SRR30186674,SRX25652378,SRS22295179,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS5dpf,GSM8448585,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing,ENS5dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf,GSM8448585,GSM8448585: ENS5dpf; Danio rerio; RNA Seq,GSM8448585 r1,GSM8448585,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26636_S4_L005_I1_001.fastq.gz FT-SA26636_S4_L005_R1_001.fastq.gz FT-SA26636_S4_L005_R2_001.fastq.gz,fastq fastq fastq,21590505830.0,69646793.0,GSM8448585 r1,0:8 1:151 2:151,A:5324745627;C:3047288539;G:3517496789;T:9140955618;N:2844913,8,151,151,,5324745627,3047288539,3517496789,9140955618,2844913,SRX25652378,SRS22295179,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System