RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

824 rows where experiment.library_source = "TRANSCRIPTOMIC", tissue_curation = "Gut" and tissue_curation_coarse = "Digestive System"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_selection 8

devstage_curation_coarse 6

devstage_curation 6

technology 5

experiment.platform 3

experiment.library_strategy 3

experiment.library_layout 2

tissue_curation_coarse 1

  • Digestive System · 824 ✖

tissue_curation 1

  • Gut · 824 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 824 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
32 32 DRR408242 DRX393848 DRS407006 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 3 zebrafish adult gut replicate 3 SAMD00529462   sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529462 DRX393848 AR019 gut 6 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529462       3546347364.0 28145614.0 DRR408242 0:126 1:0 A:919466631;C:829424335;G:818581155;T:978810217;N:65026 126 0     919466631 829424335 818581155 978810217 65026 DRX393848 DRS407006 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
33 33 DRR408241 DRX393847 DRS407005 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 2 zebrafish adult gut replicate 2 SAMD00529461   sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529461 DRX393847 AR006 gut 4 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529461       3671973648.0 29142648.0 DRR408241 0:126 1:0 A:942167543;C:859431290;G:852661772;T:1017643011;N:70032 126 0     942167543 859431290 852661772 1017643011 70032 DRX393847 DRS407005 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
34 34 DRR408240 DRX393846 DRS407004 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 1 zebrafish adult gut replicate 1 SAMD00529460   sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529460 DRX393846 AR004 gut 2 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529460       3480523704.0 27623204.0 DRR408240 0:126 1:0 A:898051986;C:827557593;G:816541244;T:938307607;N:65274 126 0     898051986 827557593 816541244 938307607 65274 DRX393846 DRS407004 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
35 35 DRR408239 DRX393845 DRS407003 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 3 zebrafish larval gut replicate 3 SAMD00529459   sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529459 DRX393845 AR012 gut 5 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529459       3463982046.0 27491921.0 DRR408239 0:126 1:0 A:842552557;C:849757648;G:837664725;T:933942026;N:65090 126 0     842552557 849757648 837664725 933942026 65090 DRX393845 DRS407003 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
36 36 DRR408238 DRX393844 DRS407002 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 2 zebrafish larval gut replicate 2 SAMD00529458   sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529458 DRX393844 AR005 gut 3 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529458       3782320416.0 30018416.0 DRR408238 0:126 1:0 A:930337206;C:920645770;G:906559955;T:1024704277;N:73208 126 0     930337206 920645770 906559955 1024704277 73208 DRX393844 DRS407002 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
37 37 DRR408237 DRX393843 DRS407001 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 1 zebrafish larval gut replicate 1 SAMD00529457   sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529457 DRX393843 AR002 gut 1 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529457       3606885828.0 28626078.0 DRR408237 0:126 1:0 A:879148446;C:885673723;G:870330963;T:971663212;N:69484 126 0     879148446 885673723 870330963 971663212 69484 DRX393843 DRS407001 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
172 172 DRR075398 DRX069312 DRS075493 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The gut of control fish 7dpf Control gut SAMD00065412   sample name:2 control gut 150701 Hiseq3A l3 018|tissue type:Gut                 Illumina HiSeq 2500 sequencing of SAMD00065412 DRX069312 Control gut 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065412       1008093492.0 28002597.0 DRR075398 0:36 A:230431417;C:251640901;G:244174255;T:281811580;N:35339 36       230431417 251640901 244174255 281811580 35339 DRX069312 DRS075493 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.9173   0.07181   0.72017   0.45193   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Gut Digestive System
9166 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 … 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. B… Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7292228.bam 5149STDY7292228.bam.bai bam bam 37970494940.0 387454030.0 E MTAB 7159:5149STDY7292228 0:98 A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108 98       11476520187 7571635167 8189594199 10701044279 31701108 ERX2797590 ERS2709706 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.87568   0.2122   0.82582   0.5259   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
9167 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 … 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. B… Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7274848.bam 5149STDY7274848.bam.bai bam bam 34517322840.0 352217580.0 E MTAB 7159:5149STDY7274848 0:98 A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273 98       10635243399 6658515314 7525079510 9695995344 2489273 ERX2797589 ERS2709705 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.86206   0.18065   0.83514   0.53609   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
9168 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 … 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. B… Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7274847.bam 5149STDY7274847.bam.bai bam bam 34467649678.0 351710711.0 E MTAB 7159:5149STDY7274847 0:98 A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266 98       10609988948 6722093635 7464497879 9667814950 3254266 ERX2797588 ERS2709704 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.88751   0.21835   0.83771   0.53927   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
9169 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 … 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. B… Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7274846.bam 5149STDY7274846.bam.bai bam bam 35052538472.0 357678964.0 E MTAB 7159:5149STDY7274846 0:98 A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277 98       10698116265 6858102477 7626019661 9866905792 3394277 ERX2797587 ERS2709703 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.88916   0.21537   0.83802   0.5336   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
24918 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 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 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 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 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 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 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 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 24926 SRR25594450 SRX21322821 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 1 1.fq K 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-1_1.fq.gz K-1_2.fq.gz fastq fastq 7164142200.0 23880474.0 K 1 1.fq.gz 0:150 1:150 A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789 150 150     1896647470 1661542391 1700422400 1905500150 29789 SRX21322821 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94635 0.94209 0.03738 0.03664 0.71961 0.72571 0.45014 0.44857 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
29041 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
32923 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 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 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 32932 SRR29498576 SRX25008876 SRS21709095 SRP515416 PRJNA1127032 Zebrafish Tissue Mid Range RNA Sequencing PRJNA1127032 Other This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.         M1g   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M1g|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 11 11 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     M1g_R2.fq.gz M1g_R1.fq.gz fastq fastq 7351182000.0 24503940.0 M1g R1.fq.gz 0:150 1:150 A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321 150 150     1623685246 1858847576 2315396486 1553169371 83321 SRX25008876 SRS21709095 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96004 0.21521 0.16113 0.04578 0.92431 0.99143 0.61867 0.63432 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Gut Digestive System
33351 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 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 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 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 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 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 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 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 33359 SRR30125642 SRX25595184 SRS22245025 SRP524094 PRJNA1144090 Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis GSE273916 Transcriptome Analysis The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.       D3 4 1 GSM8439531   source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing D3 4 1 CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample intestine   RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.   tissue:intestine GSM8439531 GSM8439531: D3 4 1; Danio rerio; RNA Seq GSM8439531 r1 GSM8439531 1 RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz fastq fastq 6996797279.0 24229469.0 GSM8439531 r1 0:144.38 1:144.39 A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723 144 144     1841905352 1647600285 1654313322 1852960597 17723 SRX25595184 SRS22245025 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
34137 34137 SRR31360761 SRX26734629 SRS23224778 SRP545397 PRJNA1186411 Zebrafish intestine sequencing PRJNA1186411 Other To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions         WT3   strain:AB|isolate:WT3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: larvae intestine WT3.fq WT3.fq nomal RAN Seq of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP545397     WT3_R1.fq.gz WT3_R2.fq.gz fastq fastq 7045875300.0 23486251.0 WT3 R1.fq.gz 0:150 1:150 A:1817741681;C:1708030651;G:1712073267;T:1808003621;N:26080 150 150     1817741681 1708030651 1712073267 1808003621 26080 SRX26734629 SRS23224778 SRA2015506 Fudan University|School of Life Sciences Fudan University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-11-15 Larval Larval Gut Digestive System
34138 34138 SRR31360762 SRX26734628 SRS23224777 SRP545397 PRJNA1186411 Zebrafish intestine sequencing PRJNA1186411 Other To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions         WT2   strain:AB|isolate:WT2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: larvae intestine WT2.fq WT2.fq nomal RAN Seq of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP545397     WT2_R1.fq.gz WT2_R2.fq.gz fastq fastq 6888570900.0 22961903.0 WT2 R1.fq.gz 0:150 1:150 A:1774584110;C:1673773734;G:1678866397;T:1761321702;N:24957 150 150     1774584110 1673773734 1678866397 1761321702 24957 SRX26734628 SRS23224777 SRA2015506 Fudan University|School of Life Sciences Fudan University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-11-15 Larval Larval Gut Digestive System
34139 34139 SRR31360763 SRX26734627 SRS23224776 SRP545397 PRJNA1186411 Zebrafish intestine sequencing PRJNA1186411 Other To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions         WT1   strain:AB|isolate:WT1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: larvae intestine WT1.fq WT1.fq nomal RAN Seq of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP545397     WT1_R1.fq.gz WT1_R2.fq.gz fastq fastq 6815123400.0 22717078.0 WT1 R1.fq.gz 0:150 1:150 A:1758536338;C:1650339290;G:1657619698;T:1748603714;N:24360 150 150     1758536338 1650339290 1657619698 1748603714 24360 SRX26734627 SRS23224776 SRA2015506 Fudan University|School of Life Sciences Fudan University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-11-15 Larval Larval Gut Digestive System
34140 34140 SRR31360764 SRX26734626 SRS23224775 SRP545397 PRJNA1186411 Zebrafish intestine sequencing PRJNA1186411 Other To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions         mu3   strain:AB|isolate:mu3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: larvae intestine mu3.fq mu3.fq nomal RAN Seq of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP545397     mu3_R1.fq.gz mu3_R2.fq.gz fastq fastq 7304650200.0 24348834.0 mu3 R1.fq.gz 0:150 1:150 A:1934717193;C:1720864609;G:1730177787;T:1918863192;N:27419 150 150     1934717193 1720864609 1730177787 1918863192 27419 SRX26734626 SRS23224775 SRA2015506 Fudan University|School of Life Sciences Fudan University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-11-15 Larval Larval Gut Digestive System
34141 34141 SRR31360765 SRX26734625 SRS23224774 SRP545397 PRJNA1186411 Zebrafish intestine sequencing PRJNA1186411 Other To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions         mu2   strain:AB|isolate:mu2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: larvae intestine mu2.fq mu2.fq nomal RAN Seq of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP545397     mu2_R1.fq.gz mu2_R2.fq.gz fastq fastq 7168114200.0 23893714.0 mu2 R1.fq.gz 0:150 1:150 A:1896004564;C:1692025000;G:1701080897;T:1878977280;N:26459 150 150     1896004564 1692025000 1701080897 1878977280 26459 SRX26734625 SRS23224774 SRA2015506 Fudan University|School of Life Sciences Fudan University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-11-15 Larval Larval Gut Digestive System
34142 34142 SRR31360766 SRX26734624 SRS23224773 SRP545397 PRJNA1186411 Zebrafish intestine sequencing PRJNA1186411 Other To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions         mu1   strain:AB|isolate:mu1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: larvae intestine mu1.fq mu1.fq nomal RAN Seq of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP545397     mu1_R1.fq.gz mu1_R2.fq.gz fastq fastq 7262664600.0 24208882.0 mu1 R1.fq.gz 0:150 1:150 A:1922666653;C:1711620445;G:1720530432;T:1907824480;N:22590 150 150     1922666653 1711620445 1720530432 1907824480 22590 SRX26734624 SRS23224773 SRA2015506 Fudan University|School of Life Sciences Fudan University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-11-15 Larval Larval Gut Digestive System
34491 34491 SRR31852177 SRX27211969 SRS23661292 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish BG rep3 GSM8703891   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing Zebrafish BG rep3 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7 GSM8703891 GSM8703891: Zebrafish BG rep3; Danio rerio; RNA Seq GSM8703891 r1 GSM8703891 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     BG_3_R1.fastq.gz BG_3_R2.fastq.gz fastq fastq 6899655382.0 22846541.0 GSM8703891 r1 0:151 1:151 A:1811966008;C:1615713130;G:1645022233;T:1826840592;N:113419 151 151     1811966008 1615713130 1645022233 1826840592 113419 SRX27211969 SRS23661292 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34492 34492 SRR31852178 SRX27211968 SRS23661291 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish BG rep2 GSM8703890   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing Zebrafish BG rep2 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7 GSM8703890 GSM8703890: Zebrafish BG rep2; Danio rerio; RNA Seq GSM8703890 r1 GSM8703890 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     BG_2_R1.fastq.gz BG_2_R2.fastq.gz fastq fastq 6320533538.0 20928919.0 GSM8703890 r1 0:151 1:151 A:1636247942;C:1501072316;G:1530315619;T:1652793962;N:103699 151 151     1636247942 1501072316 1530315619 1652793962 103699 SRX27211968 SRS23661291 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34493 34493 SRR31852179 SRX27211967 SRS23661290 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish BG rep1 GSM8703889   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing Zebrafish BG rep1 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7 GSM8703889 GSM8703889: Zebrafish BG rep1; Danio rerio; RNA Seq GSM8703889 r1 GSM8703889 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     BG_1_R1.fastq.gz BG_1_R2.fastq.gz fastq fastq 6720003132.0 22251666.0 GSM8703889 r1 0:151 1:151 A:1771169227;C:1572565291;G:1597071360;T:1779087569;N:109685 151 151     1771169227 1572565291 1597071360 1779087569 109685 SRX27211967 SRS23661290 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34494 34494 SRR31852180 SRX27211966 SRS23661289 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish EIB202 rep3 GSM8703888   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing Zebrafish EIB202 rep3 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7 GSM8703888 GSM8703888: Zebrafish EIB202 rep3; Danio rerio; RNA Seq GSM8703888 r1 GSM8703888 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     EIB202_3_R1.fastq.gz EIB202_3_R2.fastq.gz fastq fastq 6653244824.0 22030612.0 GSM8703888 r1 0:151 1:151 A:1715767195;C:1587994105;G:1617241387;T:1732132934;N:109203 151 151     1715767195 1587994105 1617241387 1732132934 109203 SRX27211966 SRS23661289 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34495 34495 SRR31852181 SRX27211965 SRS23661288 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish EIB202 rep2 GSM8703887   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing Zebrafish EIB202 rep2 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7 GSM8703887 GSM8703887: Zebrafish EIB202 rep2; Danio rerio; RNA Seq GSM8703887 r1 GSM8703887 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     EIB202_2_R1.fastq.gz EIB202_2_R2.fastq.gz fastq fastq 7203983198.0 23854249.0 GSM8703887 r1 0:151 1:151 A:1847641462;C:1731806146;G:1763208826;T:1861209998;N:116766 151 151     1847641462 1731806146 1763208826 1861209998 116766 SRX27211965 SRS23661288 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34496 34496 SRR31852182 SRX27211964 SRS23661287 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish EIB202 rep1 GSM8703886   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing Zebrafish EIB202 rep1 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7 GSM8703886 GSM8703886: Zebrafish EIB202 rep1; Danio rerio; RNA Seq GSM8703886 r1 GSM8703886 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     EIB202_1_R1.fastq.gz EIB202_1_R2.fastq.gz fastq fastq 6634863292.0 21969746.0 GSM8703886 r1 0:151 1:151 A:1708949626;C:1589664250;G:1615939413;T:1720201415;N:108588 151 151     1708949626 1589664250 1615939413 1720201415 108588 SRX27211964 SRS23661287 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34497 34497 SRR31852183 SRX27211963 SRS23661286 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish mock rep3 GSM8703885   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing Zebrafish mock rep3 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7 GSM8703885 GSM8703885: Zebrafish mock rep3; Danio rerio; RNA Seq GSM8703885 r1 GSM8703885 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     Mock_3_R1.fastq.gz Mock_3_R2.fastq.gz fastq fastq 6938479596.0 22975098.0 GSM8703885 r1 0:151 1:151 A:1771058080;C:1670207033;G:1705035413;T:1792066207;N:112863 151 151     1771058080 1670207033 1705035413 1792066207 112863 SRX27211963 SRS23661286 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34498 34498 SRR31852184 SRX27211962 SRS23661285 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish mock rep2 GSM8703884   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing Zebrafish mock rep2 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7 GSM8703884 GSM8703884: Zebrafish mock rep2; Danio rerio; RNA Seq GSM8703884 r1 GSM8703884 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     Mock_2_R1.fastq.gz Mock_2_R2.fastq.gz fastq fastq 7374531658.0 24418979.0 GSM8703884 r1 0:151 1:151 A:1885070518;C:1779385428;G:1810157081;T:1899798486;N:120145 151 151     1885070518 1779385428 1810157081 1899798486 120145 SRX27211962 SRS23661285 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34499 34499 SRR31852185 SRX27211961 SRS23661284 SRP554424 PRJNA1204310 Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish GSE285528 Transcriptome Analysis Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection       Zebrafish mock rep1 GSM8703883   source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing Zebrafish mock rep1 Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample Intestine 10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols. Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark. tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7 GSM8703883 GSM8703883: Zebrafish mock rep1; Danio rerio; RNA Seq GSM8703883 r1 GSM8703883 1 The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP554424     Mock_1_R1.fastq.gz Mock_1_R2.fastq.gz fastq fastq 6563252448.0 21732624.0 GSM8703883 r1 0:151 1:151 A:1759569033;C:1514211809;G:1536003223;T:1753362072;N:106311 151 151     1759569033 1514211809 1536003223 1753362072 106311 SRX27211961 SRS23661284 SRA2042566 Ahua lab, East China University of Science and Technology Ahua lab, East China University of Science and Technology                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-12-30 Adult Adult Gut Digestive System
34517 34517 SRR32044795 SRX27393953 SRS23824014 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr+VC 3 I   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr+VC 3 Cr+VC 3 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz fastq fastq 6773536558.0 22428929.0 Cr+VC 3.R1.raw.fastq.gz 0:151 1:151 A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278 151 151     1792253952 1581454013 1629330621 1770470694 27278 SRX27393953 SRS23824014 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34518 34518 SRR32044796 SRX27393952 SRS23824013 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr+VC 2 H   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr+VC 2 Cr+VC 2 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz fastq fastq 7449518862.0 24667281.0 Cr+VC 2.R1.raw.fastq.gz 0:151 1:151 A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119 151 151     1969693675 1748150730 1771267240 1960378098 29119 SRX27393952 SRS23824013 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34519 34519 SRR32044797 SRX27393951 SRS23824012 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr+VC 1 G   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr+VC 1 Cr+VC 1 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295   loader:fastq load.py|options: doNotUseSharq Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq fastq fastq 6865491179.0 45466829.0 Cr+VC 1.R1.raw.fastq.gz 0:151 A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474 151       1830069736 1600281531 1626303427 1808809011 27474 SRX27393951 SRS23824012 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B   usable mapping rate bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34520 34520 SRR32044798 SRX27393950 SRS23824011 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr 3 F   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr 3 Cr 3 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz fastq fastq 6069804078.0 20098689.0 Cr 3.R1.raw.fastq.gz 0:151 1:151 A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079 151 151     1603886661 1431213970 1440806224 1593873144 24079 SRX27393950 SRS23824011 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34521 34521 SRR32044799 SRX27393949 SRS23824010 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr 2 E   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr 2 Cr 2 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295   loader:fastq load.py|options: doNotUseSharq Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq fastq fastq 8327156985.0 55146735.0 Cr 2.R1.raw.fastq.gz 0:151 A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145 151       2181317777 1974793526 2003240106 2167771431 34145 SRX27393949 SRS23824010 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B   usable mapping rate bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34522 34522 SRR32044800 SRX27393948 SRS23824009 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr 1 D   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr 1 Cr 1 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz fastq fastq 7322067614.0 24245257.0 Cr 1.R1.raw.fastq.gz 0:151 1:151 A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557 151 151     1927213281 1727973559 1748866497 1917985720 28557 SRX27393948 SRS23824009 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34523 34523 SRR32044801 SRX27393947 SRS23824008 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Con 3 C   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Con 3 Con 3 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz fastq fastq 10329187314.0 34202607.0 Con 3.R1.raw.fastq.gz 0:151 1:151 A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354 151 151     2805764955 2343400161 2421657823 2758323021 41354 SRX27393947 SRS23824008 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34524 34524 SRR32044802 SRX27393946 SRS23824007 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Con 2 B   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Con 2 Con 2 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz fastq fastq 10789961398.0 35728349.0 Con 2.R1.raw.fastq.gz 0:151 1:151 A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353 151 151     2983305704 2396592872 2488165589 2921853880 43353 SRX27393946 SRS23824007 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34525 34525 SRR32044803 SRX27393945 SRS23824006 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Con 1 A   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Con 1 Con 1 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz fastq fastq 7118179260.0 23570130.0 Con 1.R1.raw.fastq.gz 0:151 1:151 A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275 151 151     1874284939 1673861890 1718740497 1851263659 28275 SRX27393945 SRS23824006 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
38009 38009 SRR1265748 SRX529142 SRS598839 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Gut Replicate 3 sRNAseq GSM1376631   source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type Singapore strain Female Gut Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Gut|genetic background:Wild type Singapore strain GSM1376631 GSM1376631: Female Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376631   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376631 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG012_TTAGGC_L008_R1.fastq.gz fastq 425902173.0 8351023.0 GSM1376631 r1 0:51 A:85733692;C:98728458;G:130104130;T:111282282;N:53611 51       85733692 98728458 130104130 111282282 53611 SRX529142 SRS598839 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00598   0.00074   0.99565   0.68818   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38010 38010 SRR1265747 SRX529141 SRS598838 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Gut Replicate 2 sRNAseq GSM1376630   source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type Singapore strain Female Gut Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Gut|genetic background:Wild type Singapore strain GSM1376630 GSM1376630: Female Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376630   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376630 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG011_CGATGT_L008_R1.fastq.gz fastq 464997192.0 9117592.0 GSM1376630 r1 0:51 A:94817360;C:107530735;G:141688278;T:120903676;N:57143 51       94817360 107530735 141688278 120903676 57143 SRX529141 SRS598838 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00297   0.00033   0.9975   0.62721   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38011 38011 SRR1265746 SRX529140 SRS598837 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Gut Replicate 1 sRNAseq GSM1376629   source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type Singapore strain Female Gut Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Gut|genetic background:Wild type Singapore strain GSM1376629 GSM1376629: Female Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376629   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376629 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG010_ATCACG_L008_R1.fastq.gz fastq 798808308.0 15662908.0 GSM1376629 r1 0:51 A:163944400;C:183125028;G:240040726;T:211597768;N:100386 51       163944400 183125028 240040726 211597768 100386 SRX529140 SRS598837 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.01106   0.00122   0.99466   0.66862   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38012 38012 SRR1265745 SRX529139 SRS598836 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Gut Replicate 3 sRNAseq GSM1376628   source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type Singapore strain Male Gut Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Gut|genetic background:Wild type Singapore strain GSM1376628 GSM1376628: Male Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376628   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376628 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG009_GCCAAT_L007_R1.fastq.gz fastq 224291778.0 4397878.0 GSM1376628 r1 0:51 A:45043664;C:58692343;G:66840019;T:53695301;N:20451 51       45043664 58692343 66840019 53695301 20451 SRX529139 SRS598836 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.0015   0.00021   0.99829   0.69477   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38013 38013 SRR1265743 SRX529138 SRS598835 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Gut Replicate 1 sRNAseq GSM1376626   source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type Singapore strain Male Gut Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Gut|genetic background:Wild type Singapore strain GSM1376626 GSM1376626: Male Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376626   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376626 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG007_TGACCA_L007_R1.fastq.gz fastq 1058961552.0 20763952.0 GSM1376626 r1 0:51 A:205056709;C:273349362;G:322710601;T:257753257;N:91623 51       205056709 273349362 322710601 257753257 91623 SRX529138 SRS598835 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00382   0.00043   0.99746   0.683   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38023 38023 SRR1265744 SRX529128 SRS598826 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Gut Replicate 2 sRNAseq GSM1376627   source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type Singapore strain Male Gut Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Gut|genetic background:Wild type Singapore strain GSM1376627 GSM1376627: Male Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376627   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376627 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG008_ACAGTG_L007_R1.fastq.gz fastq 541064457.0 10609107.0 GSM1376627 r1 0:51 A:104798947;C:136927266;G:166713427;T:132575036;N:49781 51       104798947 136927266 166713427 132575036 49781 SRX529128 SRS598826 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00679   0.00072   0.99655   0.72132   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38059 38059 SRR1524245 SRX661010 SRS665985 SRP044781 PRJNA255848 Danio rerio Transcriptome PRJNA255848 Transcriptome Analysis Transcriptome analysis of 12 zebrafish tissues parent bioproject:PRJNA255979 pubmed:27189481 Zebrafish intestine Zebrafish intestine F Dr 9   strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Intestine|BioSampleModel:Model organism or animal                 Zebrafish intestine F Dr 9 F Dr 9 Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP044781     F_Dr_9_GCCAAT_L005_R2.fastq.gz F_Dr_9_GCCAAT_L005_R1.fastq.gz fastq fastq 8637468200.0 43187341.0 F Dr 9 files 0:100 1:100 A:2270309093;C:2039596980;G:2056249938;T:2263331787;N:7980402 100 100     2270309093 2039596980 2056249938 2263331787 7980402 SRX661010 SRS665985 SRA176464 INRA|Fish Physiology and Genomics INRA PhyloFish 2 0.94661 0.94511 0.06033 0.06049 0.75743 0.75747 0.43604 0.43901 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   France 2015-07-24 Adult Adult Gut Digestive System
38269 38269 SRR1609746 SRX730399 SRS719620 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   intestine10 GSM1523041   source name:intestine|tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf intestine10 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... intestine fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf GSM1523041 GSM1523041: intestine10; Danio rerio; RNA Seq GSM1523041   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523041 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     intestine10_2.fq.gz intestine10_1.fq.gz fastq fastq 3638953000.0 18194765.0 GSM1523041 r1 0:100 1:100 A:944286084;C:877180113;G:870958371;T:946463708;N:64724 100 100     944286084 877180113 870958371 946463708 64724 SRX730399 SRS719620 SRA189240 GEO Shanghai Ocean University 2 0.95871 0.95555 0.03654 0.03737 0.77546 0.77597 0.49972 0.50867 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Gut Digestive System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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