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
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,ERR2788341,ERX2797590,ERS2709706,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7292228,SAMEA4890710,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female  1 male|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7292228 p,5149STDY7292228 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7292228.bam 5149STDY7292228.bam.bai,bam bam,37970494940.0,387454030.0,E MTAB 7159:5149STDY7292228,0:98,A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108,98,,,,11476520187,7571635167,8189594199,10701044279,31701108,ERX2797590,ERS2709706,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.87568,,0.2122,,0.82582,,0.5259,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9167,ERR2788340,ERX2797589,ERS2709705,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274848,SAMEA4890709,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274848 p,5149STDY7274848 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274848.bam 5149STDY7274848.bam.bai,bam bam,34517322840.0,352217580.0,E MTAB 7159:5149STDY7274848,0:98,A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273,98,,,,10635243399,6658515314,7525079510,9695995344,2489273,ERX2797589,ERS2709705,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.86206,,0.18065,,0.83514,,0.53609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9168,ERR2788339,ERX2797588,ERS2709704,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274847,SAMEA4890708,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274847 p,5149STDY7274847 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274847.bam 5149STDY7274847.bam.bai,bam bam,34467649678.0,351710711.0,E MTAB 7159:5149STDY7274847,0:98,A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266,98,,,,10609988948,6722093635,7464497879,9667814950,3254266,ERX2797588,ERS2709704,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88751,,0.21835,,0.83771,,0.53927,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9169,ERR2788338,ERX2797587,ERS2709703,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274846,SAMEA4890707,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274846 p,5149STDY7274846 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274846.bam 5149STDY7274846.bam.bai,bam bam,35052538472.0,357678964.0,E MTAB 7159:5149STDY7274846,0:98,A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277,98,,,,10698116265,6858102477,7626019661,9866905792,3394277,ERX2797587,ERS2709703,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88916,,0.21537,,0.83802,,0.5336,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
29041,SRR26990794,SRX22683825,SRS19677539,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut3,GSM7924158,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924158,GSM7924158: WT gut3; Danio rerio; RNA Seq,GSM7924158 r1,GSM7924158,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz,fastq fastq,6066709786.0,20088443.0,GSM7924158 r1,0:151 1:151,A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156,151,151,,,1673762656,1360901090,1385125931,1646863953,56156,SRX22683825,SRS19677539,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.92515,0.9297,0.0691,0.0659,0.75041,0.75022,0.53007,0.53064,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29042,SRR26990795,SRX22683824,SRS19677538,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut2,GSM7924157,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924157,GSM7924157: WT gut2; Danio rerio; RNA Seq,GSM7924157 r1,GSM7924157,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz,fastq fastq,5406867570.0,17903535.0,GSM7924157 r1,0:151 1:151,A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612,151,151,,,1464846243,1237183908,1259215309,1445572498,49612,SRX22683824,SRS19677538,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93795,0.94322,0.05952,0.05592,0.75933,0.75887,0.54179,0.53451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29043,SRR26990796,SRX22683823,SRS19677537,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut1,GSM7924156,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924156,GSM7924156: WT gut1; Danio rerio; RNA Seq,GSM7924156 r1,GSM7924156,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz,fastq fastq,5162192908.0,17093354.0,GSM7924156 r1,0:151 1:151,A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343,151,151,,,1404682153,1175657030,1196829496,1384975886,48343,SRX22683823,SRS19677537,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93119,0.93585,0.06122,0.05809,0.74757,0.74757,0.54124,0.54417,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29044,SRR26990797,SRX22683822,SRS19677536,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut3,GSM7924155,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924155,GSM7924155: itgavKO gut3; Danio rerio; RNA Seq,GSM7924155 r1,GSM7924155,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz,fastq fastq,4146743578.0,13730939.0,GSM7924155 r1,0:151 1:151,A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387,151,151,,,1130002132,943522869,958031732,1115146458,40387,SRX22683822,SRS19677536,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93764,0.94144,0.05938,0.05594,0.7553,0.75485,0.55535,0.55018,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29045,SRR26990798,SRX22683821,SRS19677535,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut2,GSM7924154,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924154,GSM7924154: itgavKO gut2; Danio rerio; RNA Seq,GSM7924154 r1,GSM7924154,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz,fastq fastq,4225756140.0,13992570.0,GSM7924154 r1,0:151 1:151,A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530,151,151,,,1133211420,974497998,995876972,1122129220,40530,SRX22683821,SRS19677535,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.95341,0.95884,0.05109,0.04883,0.77542,0.77368,0.51301,0.50704,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29046,SRR26990799,SRX22683820,SRS19677534,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itagvKO gut1,GSM7924153,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itagvKO gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924153,GSM7924153: itagvKO gut1; Danio rerio; RNA Seq,GSM7924153 r1,GSM7924153,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz,fastq fastq,5954117844.0,19715622.0,GSM7924153 r1,0:151 1:151,A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859,151,151,,,1600496071,1372939932,1393534700,1587094282,52859,SRX22683820,SRS19677534,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.94807,0.95298,0.05682,0.05385,0.74004,0.73925,0.54423,0.54484,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
30620,SRR27907608,SRX23567386,SRS20412878,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,pubmed:40392591,,KO12. Ctla 4 knockout,GSM8068839,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO12. Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0  https://www.gsea msigdb.org/gsea/index.jsp  and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks  the DEGs were retrieved in STRING version 11.5  https://string db.org/ database combined score > 0.4  and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068839,GSM8068839: KO12. Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068839 r1,GSM8068839,1,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO12_Clean_Data2.fq.gz KO12_Clean_Data1.fq.gz,fastq fastq,5415971621.0,18199812.0,GSM8068839 r1,0:148.79 1:148.79,A:1482389043;C:1213758088;G:1232295642;T:1487496355;N:32493,148,148,,,1482389043,1213758088,1232295642,1487496355,32493,SRX23567386,SRS20412878,SRA1799527,zhejiang university,zhejiang university,2,0.86496,0.86584,0.08493,0.08156,0.73553,0.73588,0.50941,0.5104,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30621,SRR27907609,SRX23567385,SRS20412877,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,pubmed:40392591,,KO11  Ctla 4 knockout,GSM8068838,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO11  Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0  https://www.gsea msigdb.org/gsea/index.jsp  and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks  the DEGs were retrieved in STRING version 11.5  https://string db.org/ database combined score > 0.4  and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068838,GSM8068838: KO11  Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068838 r1,GSM8068838,1,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO11_Clean_Data2.fq.gz KO11_Clean_Data1.fq.gz,fastq fastq,5443694370.0,18290488.0,GSM8068838 r1,0:148.81 1:148.81,A:1480267395;C:1230300897;G:1247791644;T:1485302181;N:32253,148,148,,,1480267395,1230300897,1247791644,1485302181,32253,SRX23567385,SRS20412877,SRA1799527,zhejiang university,zhejiang university,2,0.86445,0.86409,0.07094,0.06652,0.74738,0.74897,0.51339,0.51762,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30622,SRR27907610,SRX23567384,SRS20412876,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,pubmed:40392591,,KO9  Ctla 4 knockout,GSM8068837,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO9  Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0  https://www.gsea msigdb.org/gsea/index.jsp  and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks  the DEGs were retrieved in STRING version 11.5  https://string db.org/ database combined score > 0.4  and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068837,GSM8068837: KO9  Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068837 r1,GSM8068837,1,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO9_Clean_Data2.fq.gz KO9_Clean_Data1.fq.gz,fastq fastq,5971590749.0,20072217.0,GSM8068837 r1,0:148.76 1:148.75,A:1640322573;C:1334570646;G:1352953128;T:1643708463;N:35939,148,148,,,1640322573,1334570646,1352953128,1643708463,35939,SRX23567384,SRS20412876,SRA1799527,zhejiang university,zhejiang university,2,0.86793,0.86937,0.07855,0.07588,0.74393,0.74523,0.50694,0.51104,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30623,SRR27907611,SRX23567383,SRS20412875,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,pubmed:40392591,,WT8  control,GSM8068836,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT8  control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0  https://www.gsea msigdb.org/gsea/index.jsp  and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks  the DEGs were retrieved in STRING version 11.5  https://string db.org/ database combined score > 0.4  and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068836,GSM8068836: WT8  control; Danio rerio; RNA Seq,GSM8068836 r1,GSM8068836,1,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT8_Clean_Data1.fq.gz WT8_Clean_Data2.fq.gz,fastq fastq,5740688401.0,19287992.0,GSM8068836 r1,0:148.82 1:148.81,A:1586419463;C:1274440057;G:1291660517;T:1588132746;N:35618,148,148,,,1586419463,1274440057,1291660517,1588132746,35618,SRX23567383,SRS20412875,SRA1799527,zhejiang university,zhejiang university,2,0.85516,0.85653,0.07987,0.07551,0.74515,0.74497,0.52575,0.52057,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30624,SRR27907612,SRX23567382,SRS20412874,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,pubmed:40392591,,WT7  control,GSM8068835,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT7  control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0  https://www.gsea msigdb.org/gsea/index.jsp  and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks  the DEGs were retrieved in STRING version 11.5  https://string db.org/ database combined score > 0.4  and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068835,GSM8068835: WT7  control; Danio rerio; RNA Seq,GSM8068835 r1,GSM8068835,1,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT7_Clean_Data2.fq.gz WT7_Clean_Data1.fq.gz,fastq fastq,5810188177.0,19521216.0,GSM8068835 r1,0:148.82 1:148.81,A:1609284873;C:1285068093;G:1302652710;T:1613147856;N:34645,148,148,,,1609284873,1285068093,1302652710,1613147856,34645,SRX23567382,SRS20412874,SRA1799527,zhejiang university,zhejiang university,2,0.83558,0.83684,0.08427,0.08011,0.75741,0.75836,0.52403,0.52405,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30625,SRR27907613,SRX23567381,SRS20412873,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,pubmed:40392591,,WT1  control,GSM8068834,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT1  control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0  https://www.gsea msigdb.org/gsea/index.jsp  and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks  the DEGs were retrieved in STRING version 11.5  https://string db.org/ database combined score > 0.4  and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068834,GSM8068834: WT1  control; Danio rerio; RNA Seq,GSM8068834 r1,GSM8068834,1,Total RNAs were isolated from wild type or ctla 4 /  intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB  and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT1_Clean_Data2.fq.gz WT1_Clean_Data1.fq.gz,fastq fastq,5771161671.0,19396834.0,GSM8068834 r1,0:148.77 1:148.76,A:1593780869;C:1284499295;G:1300298518;T:1592548515;N:34474,148,148,,,1593780869,1284499295,1300298518,1592548515,34474,SRX23567381,SRS20412873,SRA1799527,zhejiang university,zhejiang university,2,0.85731,0.85944,0.0704,0.06703,0.76601,0.76607,0.53065,0.53445,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
33351,SRR30125634,SRX25595192,SRS22245033,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 3,GSM8439539,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439539,GSM8439539: SBM1 3; Danio rerio; RNA Seq,GSM8439539 r1,GSM8439539,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-3.R1.fq.gz SBM1-3.R2.fq.gz,fastq fastq,6920938402.0,24030624.0,GSM8439539 r1,0:144.00 1:144.00,A:1848518187;C:1602695225;G:1609135376;T:1860572175;N:17439,144,144,,,1848518187,1602695225,1609135376,1860572175,17439,SRX25595192,SRS22245033,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33352,SRR30125635,SRX25595191,SRS22245032,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 2,GSM8439538,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439538,GSM8439538: SBM1 2; Danio rerio; RNA Seq,GSM8439538 r1,GSM8439538,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-2.R1.fq.gz SBM1-2.R2.fq.gz,fastq fastq,6873386097.0,23812133.0,GSM8439538 r1,0:144.32 1:144.33,A:1794801562;C:1631426136;G:1638460090;T:1808681001;N:17308,144,144,,,1794801562,1631426136,1638460090,1808681001,17308,SRX25595191,SRS22245032,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33353,SRR30125636,SRX25595190,SRS22245031,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 1,GSM8439537,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439537,GSM8439537: SBM1 1; Danio rerio; RNA Seq,GSM8439537 r1,GSM8439537,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-1.R1.fq.gz SBM1-1.R2.fq.gz,fastq fastq,6893638362.0,23881631.0,GSM8439537 r1,0:144.33 1:144.33,A:1801507713;C:1634518350;G:1642455999;T:1815139080;N:17220,144,144,,,1801507713,1634518350,1642455999,1815139080,17220,SRX25595190,SRS22245031,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33354,SRR30125637,SRX25595189,SRS22245030,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 3,GSM8439536,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439536,GSM8439536: FM1 3; Danio rerio; RNA Seq,GSM8439536 r1,GSM8439536,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-3.R1.fq.gz FM1-3.R2.fq.gz,fastq fastq,6926890624.0,24044310.0,GSM8439536 r1,0:144.04 1:144.05,A:1814868011;C:1638590076;G:1645410775;T:1828004537;N:17225,144,144,,,1814868011,1638590076,1645410775,1828004537,17225,SRX25595189,SRS22245030,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33355,SRR30125638,SRX25595188,SRS22245029,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 2,GSM8439535,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439535,GSM8439535: FM1 2; Danio rerio; RNA Seq,GSM8439535 r1,GSM8439535,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-2.R1.fq.gz FM1-2.R2.fq.gz,fastq fastq,6932329149.0,24050700.0,GSM8439535 r1,0:144.12 1:144.12,A:1821635965;C:1634568957;G:1641356498;T:1834750114;N:17615,144,144,,,1821635965,1634568957,1641356498,1834750114,17615,SRX25595188,SRS22245029,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33356,SRR30125639,SRX25595187,SRS22245028,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 1,GSM8439534,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439534,GSM8439534: FM1 1; Danio rerio; RNA Seq,GSM8439534 r1,GSM8439534,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-1.R1.fq.gz FM1-1.R2.fq.gz,fastq fastq,6915521492.0,24044109.0,GSM8439534 r1,0:143.81 1:143.81,A:1851629842;C:1595942468;G:1602547587;T:1865384194;N:17401,143,143,,,1851629842,1595942468,1602547587,1865384194,17401,SRX25595187,SRS22245028,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33357,SRR30125640,SRX25595186,SRS22245027,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 3,GSM8439533,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439533,GSM8439533: D3 4 3; Danio rerio; RNA Seq,GSM8439533 r1,GSM8439533,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-3.R1.fq.gz D3-4-3.R2.fq.gz,fastq fastq,6934859246.0,24095045.0,GSM8439533 r1,0:143.91 1:143.91,A:1815846879;C:1641161510;G:1648091770;T:1829741658;N:17429,143,143,,,1815846879,1641161510,1648091770,1829741658,17429,SRX25595186,SRS22245027,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33358,SRR30125641,SRX25595185,SRS22245026,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 2,GSM8439532,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439532,GSM8439532: D3 4 2; Danio rerio; RNA Seq,GSM8439532 r1,GSM8439532,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-2.R1.fq.gz D3-4-2.R2.fq.gz,fastq fastq,7053487385.0,24519028.0,GSM8439532 r1,0:143.83 1:143.84,A:1888591272;C:1630003556;G:1636509489;T:1898365125;N:17943,143,143,,,1888591272,1630003556,1636509489,1898365125,17943,SRX25595185,SRS22245026,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33359,SRR30125642,SRX25595184,SRS22245025,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics  ß  ß Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 1,GSM8439531,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439531,GSM8439531: D3 4 1; Danio rerio; RNA Seq,GSM8439531 r1,GSM8439531,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz,fastq fastq,6996797279.0,24229469.0,GSM8439531 r1,0:144.38 1:144.39,A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723,144,144,,,1841905352,1647600285,1654313322,1852960597,17723,SRX25595184,SRS22245025,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
34137,SRR31360761,SRX26734629,SRS23224778,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT3,,strain:AB|isolate:WT3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT3.fq,WT3.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT3_R1.fq.gz WT3_R2.fq.gz,fastq fastq,7045875300.0,23486251.0,WT3 R1.fq.gz,0:150 1:150,A:1817741681;C:1708030651;G:1712073267;T:1808003621;N:26080,150,150,,,1817741681,1708030651,1712073267,1808003621,26080,SRX26734629,SRS23224778,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34138,SRR31360762,SRX26734628,SRS23224777,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT2,,strain:AB|isolate:WT2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT2.fq,WT2.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT2_R1.fq.gz WT2_R2.fq.gz,fastq fastq,6888570900.0,22961903.0,WT2 R1.fq.gz,0:150 1:150,A:1774584110;C:1673773734;G:1678866397;T:1761321702;N:24957,150,150,,,1774584110,1673773734,1678866397,1761321702,24957,SRX26734628,SRS23224777,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34139,SRR31360763,SRX26734627,SRS23224776,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT1,,strain:AB|isolate:WT1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT1.fq,WT1.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT1_R1.fq.gz WT1_R2.fq.gz,fastq fastq,6815123400.0,22717078.0,WT1 R1.fq.gz,0:150 1:150,A:1758536338;C:1650339290;G:1657619698;T:1748603714;N:24360,150,150,,,1758536338,1650339290,1657619698,1748603714,24360,SRX26734627,SRS23224776,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34140,SRR31360764,SRX26734626,SRS23224775,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu3,,strain:AB|isolate:mu3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu3.fq,mu3.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu3_R1.fq.gz mu3_R2.fq.gz,fastq fastq,7304650200.0,24348834.0,mu3 R1.fq.gz,0:150 1:150,A:1934717193;C:1720864609;G:1730177787;T:1918863192;N:27419,150,150,,,1934717193,1720864609,1730177787,1918863192,27419,SRX26734626,SRS23224775,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34141,SRR31360765,SRX26734625,SRS23224774,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu2,,strain:AB|isolate:mu2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu2.fq,mu2.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu2_R1.fq.gz mu2_R2.fq.gz,fastq fastq,7168114200.0,23893714.0,mu2 R1.fq.gz,0:150 1:150,A:1896004564;C:1692025000;G:1701080897;T:1878977280;N:26459,150,150,,,1896004564,1692025000,1701080897,1878977280,26459,SRX26734625,SRS23224774,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34142,SRR31360766,SRX26734624,SRS23224773,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu1,,strain:AB|isolate:mu1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu1.fq,mu1.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu1_R1.fq.gz mu1_R2.fq.gz,fastq fastq,7262664600.0,24208882.0,mu1 R1.fq.gz,0:150 1:150,A:1922666653;C:1711620445;G:1720530432;T:1907824480;N:22590,150,150,,,1922666653,1711620445,1720530432,1907824480,22590,SRX26734624,SRS23224773,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34491,SRR31852177,SRX27211969,SRS23661292,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  BG  rep3,GSM8703891,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  BG  rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703891,GSM8703891: Zebrafish  BG  rep3; Danio rerio; RNA Seq,GSM8703891 r1,GSM8703891,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_3_R1.fastq.gz BG_3_R2.fastq.gz,fastq fastq,6899655382.0,22846541.0,GSM8703891 r1,0:151 1:151,A:1811966008;C:1615713130;G:1645022233;T:1826840592;N:113419,151,151,,,1811966008,1615713130,1645022233,1826840592,113419,SRX27211969,SRS23661292,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34492,SRR31852178,SRX27211968,SRS23661291,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  BG  rep2,GSM8703890,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  BG  rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703890,GSM8703890: Zebrafish  BG  rep2; Danio rerio; RNA Seq,GSM8703890 r1,GSM8703890,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_2_R1.fastq.gz BG_2_R2.fastq.gz,fastq fastq,6320533538.0,20928919.0,GSM8703890 r1,0:151 1:151,A:1636247942;C:1501072316;G:1530315619;T:1652793962;N:103699,151,151,,,1636247942,1501072316,1530315619,1652793962,103699,SRX27211968,SRS23661291,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34493,SRR31852179,SRX27211967,SRS23661290,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  BG  rep1,GSM8703889,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  BG  rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703889,GSM8703889: Zebrafish  BG  rep1; Danio rerio; RNA Seq,GSM8703889 r1,GSM8703889,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_1_R1.fastq.gz BG_1_R2.fastq.gz,fastq fastq,6720003132.0,22251666.0,GSM8703889 r1,0:151 1:151,A:1771169227;C:1572565291;G:1597071360;T:1779087569;N:109685,151,151,,,1771169227,1572565291,1597071360,1779087569,109685,SRX27211967,SRS23661290,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34494,SRR31852180,SRX27211966,SRS23661289,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  EIB202  rep3,GSM8703888,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  EIB202  rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703888,GSM8703888: Zebrafish  EIB202  rep3; Danio rerio; RNA Seq,GSM8703888 r1,GSM8703888,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_3_R1.fastq.gz EIB202_3_R2.fastq.gz,fastq fastq,6653244824.0,22030612.0,GSM8703888 r1,0:151 1:151,A:1715767195;C:1587994105;G:1617241387;T:1732132934;N:109203,151,151,,,1715767195,1587994105,1617241387,1732132934,109203,SRX27211966,SRS23661289,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34495,SRR31852181,SRX27211965,SRS23661288,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  EIB202  rep2,GSM8703887,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  EIB202  rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703887,GSM8703887: Zebrafish  EIB202  rep2; Danio rerio; RNA Seq,GSM8703887 r1,GSM8703887,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_2_R1.fastq.gz EIB202_2_R2.fastq.gz,fastq fastq,7203983198.0,23854249.0,GSM8703887 r1,0:151 1:151,A:1847641462;C:1731806146;G:1763208826;T:1861209998;N:116766,151,151,,,1847641462,1731806146,1763208826,1861209998,116766,SRX27211965,SRS23661288,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34496,SRR31852182,SRX27211964,SRS23661287,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  EIB202  rep1,GSM8703886,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  EIB202  rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703886,GSM8703886: Zebrafish  EIB202  rep1; Danio rerio; RNA Seq,GSM8703886 r1,GSM8703886,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_1_R1.fastq.gz EIB202_1_R2.fastq.gz,fastq fastq,6634863292.0,21969746.0,GSM8703886 r1,0:151 1:151,A:1708949626;C:1589664250;G:1615939413;T:1720201415;N:108588,151,151,,,1708949626,1589664250,1615939413,1720201415,108588,SRX27211964,SRS23661287,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34497,SRR31852183,SRX27211963,SRS23661286,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  mock  rep3,GSM8703885,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  mock  rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703885,GSM8703885: Zebrafish  mock  rep3; Danio rerio; RNA Seq,GSM8703885 r1,GSM8703885,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_3_R1.fastq.gz Mock_3_R2.fastq.gz,fastq fastq,6938479596.0,22975098.0,GSM8703885 r1,0:151 1:151,A:1771058080;C:1670207033;G:1705035413;T:1792066207;N:112863,151,151,,,1771058080,1670207033,1705035413,1792066207,112863,SRX27211963,SRS23661286,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34498,SRR31852184,SRX27211962,SRS23661285,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  mock  rep2,GSM8703884,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  mock  rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703884,GSM8703884: Zebrafish  mock  rep2; Danio rerio; RNA Seq,GSM8703884 r1,GSM8703884,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_2_R1.fastq.gz Mock_2_R2.fastq.gz,fastq fastq,7374531658.0,24418979.0,GSM8703884 r1,0:151 1:151,A:1885070518;C:1779385428;G:1810157081;T:1899798486;N:120145,151,151,,,1885070518,1779385428,1810157081,1899798486,120145,SRX27211962,SRS23661285,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34499,SRR31852185,SRX27211961,SRS23661284,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish  mock  rep1,GSM8703883,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish  mock  rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703883,GSM8703883: Zebrafish  mock  rep1; Danio rerio; RNA Seq,GSM8703883 r1,GSM8703883,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_1_R1.fastq.gz Mock_1_R2.fastq.gz,fastq fastq,6563252448.0,21732624.0,GSM8703883 r1,0:151 1:151,A:1759569033;C:1514211809;G:1536003223;T:1753362072;N:106311,151,151,,,1759569033,1514211809,1536003223,1753362072,106311,SRX27211961,SRS23661284,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34517,SRR32044795,SRX27393953,SRS23824014,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 3,I,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 3,Cr+VC 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz,fastq fastq,6773536558.0,22428929.0,Cr+VC 3.R1.raw.fastq.gz,0:151 1:151,A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278,151,151,,,1792253952,1581454013,1629330621,1770470694,27278,SRX27393953,SRS23824014,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34518,SRR32044796,SRX27393952,SRS23824013,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 2,H,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 2,Cr+VC 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz,fastq fastq,7449518862.0,24667281.0,Cr+VC 2.R1.raw.fastq.gz,0:151 1:151,A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119,151,151,,,1969693675,1748150730,1771267240,1960378098,29119,SRX27393952,SRS23824013,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34519,SRR32044797,SRX27393951,SRS23824012,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 1,G,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 1,Cr+VC 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options:  doNotUseSharq,Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq,fastq fastq,6865491179.0,45466829.0,Cr+VC 1.R1.raw.fastq.gz,0:151,A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474,151,,,,1830069736,1600281531,1626303427,1808809011,27474,SRX27393951,SRS23824012,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34520,SRR32044798,SRX27393950,SRS23824011,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 3,F,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 3,Cr 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz,fastq fastq,6069804078.0,20098689.0,Cr 3.R1.raw.fastq.gz,0:151 1:151,A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079,151,151,,,1603886661,1431213970,1440806224,1593873144,24079,SRX27393950,SRS23824011,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34521,SRR32044799,SRX27393949,SRS23824010,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 2,E,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 2,Cr 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options:  doNotUseSharq,Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq,fastq fastq,8327156985.0,55146735.0,Cr 2.R1.raw.fastq.gz,0:151,A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145,151,,,,2181317777,1974793526,2003240106,2167771431,34145,SRX27393949,SRS23824010,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34522,SRR32044800,SRX27393948,SRS23824009,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 1,D,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 1,Cr 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz,fastq fastq,7322067614.0,24245257.0,Cr 1.R1.raw.fastq.gz,0:151 1:151,A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557,151,151,,,1927213281,1727973559,1748866497,1917985720,28557,SRX27393948,SRS23824009,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34523,SRR32044801,SRX27393947,SRS23824008,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 3,C,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 3,Con 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz,fastq fastq,10329187314.0,34202607.0,Con 3.R1.raw.fastq.gz,0:151 1:151,A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354,151,151,,,2805764955,2343400161,2421657823,2758323021,41354,SRX27393947,SRS23824008,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34524,SRR32044802,SRX27393946,SRS23824007,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 2,B,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 2,Con 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz,fastq fastq,10789961398.0,35728349.0,Con 2.R1.raw.fastq.gz,0:151 1:151,A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353,151,151,,,2983305704,2396592872,2488165589,2921853880,43353,SRX27393946,SRS23824007,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34525,SRR32044803,SRX27393945,SRS23824006,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 1,A,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 1,Con 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz,fastq fastq,7118179260.0,23570130.0,Con 1.R1.raw.fastq.gz,0:151 1:151,A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275,151,151,,,1874284939,1673861890,1718740497,1851263659,28275,SRX27393945,SRS23824006,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
38059,SRR1524245,SRX661010,SRS665985,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish intestine,Zebrafish intestine,F Dr 9,,strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish intestine,F Dr 9,F Dr 9,Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP044781,,,F_Dr_9_GCCAAT_L005_R2.fastq.gz F_Dr_9_GCCAAT_L005_R1.fastq.gz,fastq fastq,8637468200.0,43187341.0,F Dr 9 files,0:100 1:100,A:2270309093;C:2039596980;G:2056249938;T:2263331787;N:7980402,100,100,,,2270309093,2039596980,2056249938,2263331787,7980402,SRX661010,SRS665985,SRA176464,INRA|Fish Physiology and Genomics,INRA PhyloFish,2,0.94661,0.94511,0.06033,0.06049,0.75743,0.75747,0.43604,0.43901,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,France,2015-07-24,Adult,Adult,Gut,Digestive System
38269,SRR1609746,SRX730399,SRS719620,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine10,GSM1523041,,source name:intestine|tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf,intestine10,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf,GSM1523041,GSM1523041: intestine10; Danio rerio; RNA Seq,GSM1523041,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523041,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine10_2.fq.gz intestine10_1.fq.gz,fastq fastq,3638953000.0,18194765.0,GSM1523041 r1,0:100 1:100,A:944286084;C:877180113;G:870958371;T:946463708;N:64724,100,100,,,944286084,877180113,870958371,946463708,64724,SRX730399,SRS719620,SRA189240,GEO,Shanghai Ocean University,2,0.95871,0.95555,0.03654,0.03737,0.77546,0.77597,0.49972,0.50867,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
38270,SRR1609745,SRX730398,SRS719619,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine18,GSM1523040,,source name:intestine|tissue:intestine|temperature:18°C|strain:Tubingen|age:6 mpf,intestine18,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:18°C|strain:Tubingen|age:6 mpf,GSM1523040,GSM1523040: intestine18; Danio rerio; RNA Seq,GSM1523040,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523040,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine18_1.fq.gz intestine18_2.fq.gz,fastq fastq,3870426800.0,19352134.0,GSM1523040 r1,0:100 1:100,A:1034436410;C:900862332;G:899347839;T:1035707094;N:73125,100,100,,,1034436410,900862332,899347839,1035707094,73125,SRX730398,SRS719619,SRA189240,GEO,Shanghai Ocean University,2,0.93279,0.92997,0.0455,0.04571,0.76152,0.76228,0.44545,0.44882,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
38271,SRR1609744,SRX730397,SRS719618,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine28,GSM1523039,,source name:intestine|tissue:intestine|temperature:28°C|strain:Tubingen|age:6 mpf,intestine28,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:28°C|strain:Tubingen|age:6 mpf,GSM1523039,GSM1523039: intestine28; Danio rerio; RNA Seq,GSM1523039,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine28_1.fq.gz intestine28_2.fq.gz,fastq fastq,3710350200.0,18551751.0,GSM1523039 r1,0:100 1:100,A:987499090;C:870092319;G:865419689;T:987267641;N:71461,100,100,,,987499090,870092319,865419689,987267641,71461,SRX730397,SRS719618,SRA189240,GEO,Shanghai Ocean University,2,0.94613,0.94058,0.04736,0.04784,0.7599,0.76288,0.51653,0.51797,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
41072,SRR3655801,SRX1836012,SRS1495476,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,GSM2195935,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195935,GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq,GSM2195935,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS410.fastq.gz,fastq,1402184556.0,18692635.0,GSM2195935 r1,0:75.01 1:0,A:363262740;C:326626075;G:322630446;T:389582075;N:83220,75,0,,,363262740,326626075,322630446,389582075,83220,SRX1836012,SRS1495476,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92115,,0.08008,,0.7389,,0.52691,,73,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41073,SRR3655802,SRX1836012,SRS1495476,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,GSM2195935,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195935,GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq,GSM2195935,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS410.fastq.gz,fastq,3450884531.0,46005067.0,GSM2195935 r2,0:75.01 1:0,A:874448337;C:808236306;G:797225707;T:970673048;N:301133,75,0,,,874448337,808236306,797225707,970673048,301133,SRX1836012,SRS1495476,SRA432774,GEO,Children's Hospital Los Angeles,1,0.93035,,0.08192,,0.73271,,0.52273,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41074,SRR3655799,SRX1836011,SRS1495475,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,GSM2195934,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195934,GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq,GSM2195934,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195934,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS409.fastq.gz,fastq,1422635421.0,18963577.0,GSM2195934 r1,0:75.02 1:0,A:362173330;C:332883466;G:329078937;T:398420070;N:79618,75,0,,,362173330,332883466,329078937,398420070,79618,SRX1836011,SRS1495475,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92474,,0.07466,,0.73423,,0.50871,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41075,SRR3655800,SRX1836011,SRS1495475,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,GSM2195934,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195934,GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq,GSM2195934,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195934,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS409.fastq.gz,fastq,3549432159.0,47315580.0,GSM2195934 r2,0:75.02 1:0,A:893492844;C:832741437;G:822208498;T:1000698758;N:290622,75,0,,,893492844,832741437,822208498,1000698758,290622,SRX1836011,SRS1495475,SRA432774,GEO,Children's Hospital Los Angeles,1,0.93197,,0.07554,,0.73109,,0.50825,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41076,SRR3655797,SRX1836010,SRS1495474,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,GSM2195933,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195933,GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq,GSM2195933,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195933,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS408.fastq.gz,fastq,1400640841.0,18670640.0,GSM2195933 r1,0:75.02 1:0,A:363544908;C:324586412;G:320620988;T:391797091;N:91442,75,0,,,363544908,324586412,320620988,391797091,91442,SRX1836010,SRS1495474,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92971,,0.10926,,0.73016,,0.51418,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41077,SRR3655798,SRX1836010,SRS1495474,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,GSM2195933,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195933,GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq,GSM2195933,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195933,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS408.fastq.gz,fastq,1400640841.0,18670640.0,GSM2195933 r2,0:75.02 1:0,A:363544908;C:324586412;G:320620988;T:391797091;N:91442,75,0,,,363544908,324586412,320620988,391797091,91442,SRX1836010,SRS1495474,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92977,,0.10933,,0.73008,,0.51355,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41078,SRR3655795,SRX1836009,SRS1495472,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,GSM2195932,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195932,GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq,GSM2195932,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS383.fastq.gz,fastq,1510741670.0,20138480.0,GSM2195932 r1,0:75.02 1:0,A:374411447;C:361418430;G:359803924;T:415021333;N:86536,75,0,,,374411447,361418430,359803924,415021333,86536,SRX1836009,SRS1495472,SRA432774,GEO,Children's Hospital Los Angeles,1,0.94789,,0.05269,,0.77753,,0.53939,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41079,SRR3655796,SRX1836009,SRS1495472,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,GSM2195932,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195932,GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq,GSM2195932,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS383.fastq.gz,fastq,3623681121.0,48303841.0,GSM2195932 r2,0:75.02 1:0,A:881893112;C:869893713;G:867139931;T:1004485159;N:269206,75,0,,,881893112,869893713,867139931,1004485159,269206,SRX1836009,SRS1495472,SRA432774,GEO,Children's Hospital Los Angeles,1,0.95546,,0.05225,,0.77218,,0.53519,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41080,SRR3655793,SRX1836008,SRS1495473,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,GSM2195931,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195931,GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq,GSM2195931,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS381.fastq.gz,fastq,1348860046.0,17985061.0,GSM2195931 r1,0:75.00 1:0,A:350940564;C:313266568;G:309387786;T:375159308;N:105820,75,0,,,350940564,313266568,309387786,375159308,105820,SRX1836008,SRS1495473,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92348,,0.06356,,0.77252,,0.52707,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41081,SRR3655794,SRX1836008,SRS1495473,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,GSM2195931,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195931,GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq,GSM2195931,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS381.fastq.gz,fastq,3298786881.0,43979655.0,GSM2195931 r2,0:75.01 1:0,A:829523096;C:775146066;G:763427556;T:930352935;N:337228,75,0,,,829523096,775146066,763427556,930352935,337228,SRX1836008,SRS1495473,SRA432774,GEO,Children's Hospital Los Angeles,1,0.9361,,0.06336,,0.76353,,0.54746,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41082,SRR3655791,SRX1836007,SRS1495471,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,GSM2195930,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195930,GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq,GSM2195930,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS380.fastq.gz,fastq,1448364484.0,19307379.0,GSM2195930 r1,0:75.02 1:0,A:359052072;C:343824905;G:344804667;T:400589883;N:92957,75,0,,,359052072,343824905,344804667,400589883,92957,SRX1836007,SRS1495471,SRA432774,GEO,Children's Hospital Los Angeles,1,0.94277,,0.05284,,0.77881,,0.57769,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41083,SRR3655792,SRX1836007,SRS1495471,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,GSM2195930,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195930,GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq,GSM2195930,,1,Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS380.fastq.gz,fastq,3599154025.0,47976708.0,GSM2195930 r2,0:75.02 1:0,A:875615940;C:857379635;G:859609503;T:1006260031;N:288916,75,0,,,875615940,857379635,859609503,1006260031,288916,SRX1836007,SRS1495471,SRA432774,GEO,Children's Hospital Los Angeles,1,0.95037,,0.0525,,0.77147,,0.5711,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41575,SRR5045902,SRX2368488,SRS1814332,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutCV 2,GSM2401374,,source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutCV 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401374,GSM2401374: MutCV 2; Danio rerio; RNA Seq,GSM2401374,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401374,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutCV_2.fastq,fastq,3876906576.0,76017776.0,GSM2401374 r1,0:51 1:0,A:957781980;C:915286453;G:859927041;T:1143804372;N:106730,51,0,,,957781980,915286453,859927041,1143804372,106730,SRX2368488,SRS1814332,SRA497672,GEO,Duke University School of Medicine,1,0.96196,,0.11375,,0.70887,,0.53406,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41576,SRR5045901,SRX2368487,SRS1814330,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutCV 1,GSM2401373,,source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutCV 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401373,GSM2401373: MutCV 1; Danio rerio; RNA Seq,GSM2401373,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401373,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutCV_1.fastq,fastq,3835824444.0,75212244.0,GSM2401373 r1,0:51 1:0,A:946407906;C:904393791;G:851683286;T:1133241327;N:98134,51,0,,,946407906,904393791,851683286,1133241327,98134,SRX2368487,SRS1814330,SRA497672,GEO,Duke University School of Medicine,1,0.95795,,0.11761,,0.70481,,0.53357,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41577,SRR5045900,SRX2368486,SRS1814331,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutGF 2,GSM2401372,,source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutGF 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401372,GSM2401372: MutGF 2; Danio rerio; RNA Seq,GSM2401372,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401372,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutGF_2.fastq,fastq,3299677866.0,64699566.0,GSM2401372 r1,0:51 1:0,A:809247440;C:784035543;G:731742820;T:974610541;N:41522,51,0,,,809247440,784035543,731742820,974610541,41522,SRX2368486,SRS1814331,SRA497672,GEO,Duke University School of Medicine,1,0.96247,,0.1049,,0.74034,,0.5525,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41578,SRR5045899,SRX2368485,SRS1814329,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutGF 1,GSM2401371,,source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutGF 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401371,GSM2401371: MutGF 1; Danio rerio; RNA Seq,GSM2401371,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401371,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutGF_1.fastq,fastq,3734921199.0,73233749.0,GSM2401371 r1,0:51 1:0,A:923493830;C:879193170;G:840678282;T:1091454504;N:101413,51,0,,,923493830,879193170,840678282,1091454504,101413,SRX2368485,SRS1814329,SRA497672,GEO,Duke University School of Medicine,1,0.96328,,0.1099,,0.73492,,0.50455,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41579,SRR5045898,SRX2368484,SRS1814328,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 3,GSM2401370,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 3,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401370,GSM2401370: WTCV 3; Danio rerio; RNA Seq,GSM2401370,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_3.fastq,fastq,3928418412.0,77027812.0,GSM2401370 r1,0:51 1:0,A:966197912;C:939595492;G:912123411;T:1110393846;N:107751,51,0,,,966197912,939595492,912123411,1110393846,107751,SRX2368484,SRS1814328,SRA497672,GEO,Duke University School of Medicine,1,0.97188,,0.08862,,0.7357,,0.53339,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41580,SRR5045897,SRX2368483,SRS1814327,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 2,GSM2401369,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401369,GSM2401369: WTCV 2; Danio rerio; RNA Seq,GSM2401369,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_2.fastq,fastq,3782941473.0,74175323.0,GSM2401369 r1,0:51 1:0,A:928563733;C:910471684;G:872137892;T:1071716851;N:51313,51,0,,,928563733,910471684,872137892,1071716851,51313,SRX2368483,SRS1814327,SRA497672,GEO,Duke University School of Medicine,1,0.97097,,0.09668,,0.74255,,0.55455,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41581,SRR5045896,SRX2368482,SRS1814326,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 1,GSM2401368,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401368,GSM2401368: WTCV 1; Danio rerio; RNA Seq,GSM2401368,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_1.fastq,fastq,3643146954.0,71434254.0,GSM2401368 r1,0:51 1:0,A:877377891;C:875020597;G:839793450;T:1050862579;N:92437,51,0,,,877377891,875020597,839793450,1050862579,92437,SRX2368482,SRS1814326,SRA497672,GEO,Duke University School of Medicine,1,0.9683,,0.08514,,0.73525,,0.55486,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41582,SRR5045895,SRX2368481,SRS1814325,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 3,GSM2401367,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 3,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401367,GSM2401367: WTGF 3; Danio rerio; RNA Seq,GSM2401367,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401367,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_3.fastq,fastq,3462802386.0,67898086.0,GSM2401367 r1,0:51 1:0,A:843407439;C:830117704;G:803633976;T:985548502;N:94765,51,0,,,843407439,830117704,803633976,985548502,94765,SRX2368481,SRS1814325,SRA497672,GEO,Duke University School of Medicine,1,0.97202,,0.08623,,0.75939,,0.56558,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41583,SRR5045894,SRX2368480,SRS1814324,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 2,GSM2401366,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401366,GSM2401366: WTGF 2; Danio rerio; RNA Seq,GSM2401366,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401366,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_2.fastq,fastq,3699149799.0,72532349.0,GSM2401366 r1,0:51 1:0,A:907425678;C:884609705;G:855651232;T:1051368070;N:95114,51,0,,,907425678,884609705,855651232,1051368070,95114,SRX2368480,SRS1814324,SRA497672,GEO,Duke University School of Medicine,1,0.96861,,0.08856,,0.75223,,0.55327,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41584,SRR5045893,SRX2368479,SRS1814323,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 1,GSM2401365,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401365,GSM2401365: WTGF 1; Danio rerio; RNA Seq,GSM2401365,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401365,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_1.fastq,fastq,3948593247.0,77423397.0,GSM2401365 r1,0:51 1:0,A:951060123;C:949871425;G:909862458;T:1137745436;N:53805,51,0,,,951060123,949871425,909862458,1137745436,53805,SRX2368479,SRS1814323,SRA497672,GEO,Duke University School of Medicine,1,0.97252,,0.08483,,0.74418,,0.54605,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41844,SRR5259817,SRX2564548,SRS1981207,SRP099850,PRJNA374872,Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish],GSE94933,Other,We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish,parent bioproject:PRJNA374867,pubmed:28850571,,zIEC3 mRNA,GSM2492108,,tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,zIEC3 mRNA,Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information,Intestinal Epithelial Cells RNA seq,,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets,strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,GSM2492108,GSM2492108: zIEC3 mRNA; Danio rerio; RNA Seq,GSM2492108,,1,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,GEO Accession:GSM2492108,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP099850,,,ZIEC3_GCCAAT_L001_R2_001.fastq.gz ZIEC3_GCCAAT_L001_R1_001.fastq.gz,fastq fastq,2644689216.0,27548846.0,GSM2492108 r1,0:48 1:48,A:687890725;C:632255900;G:620389531;T:703494916;N:658144,48,48,,,687890725,632255900,620389531,703494916,658144,SRX2564548,SRS1981207,SRA538156,GEO,"John Rawls, Duke University",2,0.87587,0.87862,0.06582,0.06632,0.73931,0.73878,0.53496,0.53653,48,48,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-02-15,Adult,Adult,Gut,Digestive System
41845,SRR5259816,SRX2564547,SRS1981208,SRP099850,PRJNA374872,Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish],GSE94933,Other,We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish,parent bioproject:PRJNA374867,pubmed:28850571,,zIEC2 mRNA,GSM2492107,,tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,zIEC2 mRNA,Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information,Intestinal Epithelial Cells RNA seq,,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets,strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,GSM2492107,GSM2492107: zIEC2 mRNA; Danio rerio; RNA Seq,GSM2492107,,1,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,GEO Accession:GSM2492107,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP099850,,,ZIEC2_GCCAAT_L005_R1_001.fastq.gz ZIEC2_GCCAAT_L005_R2_001.fastq.gz,fastq fastq,1785594816.0,18599946.0,GSM2492107 r1,0:48 1:48,A:466092820;C:422828003;G:420238032;T:476324795;N:111166,48,48,,,466092820,422828003,420238032,476324795,111166,SRX2564547,SRS1981208,SRA538156,GEO,"John Rawls, Duke University",2,0.85545,0.86359,0.08337,0.08488,0.74635,0.74677,0.52663,0.53064,48,48,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-02-15,Adult,Adult,Gut,Digestive System
41846,SRR5259815,SRX2564546,SRS1981206,SRP099850,PRJNA374872,Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish],GSE94933,Other,We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish,parent bioproject:PRJNA374867,pubmed:28850571,,zIEC1 mRNA,GSM2492106,,tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,zIEC1 mRNA,Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information,Intestinal Epithelial Cells RNA seq,,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets,strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells,GSM2492106,GSM2492106: zIEC1 mRNA; Danio rerio; RNA Seq,GSM2492106,,1,To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.,GEO Accession:GSM2492106,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP099850,,,ZIEC1_CGATGT_L004_R1_001.fastq.gz ZIEC1_CGATGT_L004_R2_001.fastq.gz,fastq fastq,1953396576.0,20347881.0,GSM2492106 r1,0:48 1:48,A:510243495;C:461085497;G:464477553;T:517509152;N:80879,48,48,,,510243495,461085497,464477553,517509152,80879,SRX2564546,SRS1981206,SRA538156,GEO,"John Rawls, Duke University",2,0.87991,0.88564,0.09576,0.0974,0.74789,0.74909,0.54326,0.54368,48,48,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-02-15,Adult,Adult,Gut,Digestive System
44033,SRR6231893,SRX3340325,SRS2641976,SRP122541,PRJNA415856,Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment,PRJNA415856,Transcriptome Analysis,Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.,,pubmed:28403821,,GFP positive cells,en GFP positive JK,,strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal neurons|BioSampleModel:Model organism or animal,,,,,,,,,en GFP positive JK r1,en GFP positive JK r1 fwd,en GFP positive JK r1 fwd,The library was prepapred by the Iowa State DNA facility.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP122541,,,d7phoGFPA_GCCAAT_R1_001.fastq.gz d7phoGFPA_GCCAAT_R2_001.fastq.gz,fastq fastq,22618935400.0,113094677.0,d7phoGFPA GCCAAT R1 001.fastq.gz,0:100 1:100,A:6233619158;C:5097706589;G:5045972110;T:6222785585;N:18851958,100,100,,,6233619158,5097706589,5045972110,6222785585,18851958,SRX3340325,SRS2641976,SRA625723,Iowa State University|Genetics Development and Cell Biology,Iowa State University,2,0.91266,0.9056,0.16638,0.16643,0.68008,0.68367,0.48483,0.48254,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-10-27,Larval,Larval,Gut,Digestive System
44034,SRR6231894,SRX3340324,SRS2641976,SRP122541,PRJNA415856,Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment,PRJNA415856,Transcriptome Analysis,Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.,,pubmed:28403821,,GFP positive cells,en GFP positive JK,,strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal neurons|BioSampleModel:Model organism or animal,,,,,,,,,en GFP positive JK r2,en GFP positive JK r2 fwd,en GFP positive JK r2 fwd,The library was prepapred by the Iowa State DNA facility.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP122541,,,d7phoGFPB_GTGAAA_R2_001.fastq.gz d7phoGFPB_GTGAAA_R1_001.fastq.gz,fastq fastq,13753541400.0,68767707.0,d7phoGFPB GTGAAA R1 001.fastq.gz,0:100 1:100,A:3807602619;C:3077358417;G:3063510819;T:3793560543;N:11509002,100,100,,,3807602619,3077358417,3063510819,3793560543,11509002,SRX3340324,SRS2641976,SRA625723,Iowa State University|Genetics Development and Cell Biology,Iowa State University,2,0.90465,0.89478,0.20689,0.2048,0.68402,0.68738,0.4887,0.48279,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-10-27,Larval,Larval,Gut,Digestive System
44035,SRR6231895,SRX3340323,SRS2641979,SRP122541,PRJNA415856,Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment,PRJNA415856,Transcriptome Analysis,Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.,,pubmed:28403821,,GFP negative cells,en GFP negative JK,,strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal non neurons|BioSampleModel:Model organism or animal,,,,,,,,,en GFP negative JK r1,en GFP negative JK r1 fwd,en GFP negative JK r1 fwd,The library was prepapred by the Iowa State DNA facility.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP122541,,,d7phoGFP-A_ACAGTG_R1_001.fastq.gz d7phoGFP-A_ACAGTG_R2_001.fastq.gz,fastq fastq,17591029600.0,87955148.0,d7phoGFP A ACAGTG R2 001.fastq.gz,0:100 1:100,A:4757105599;C:4046056704;G:4012427038;T:4760767597;N:14672662,100,100,,,4757105599,4046056704,4012427038,4760767597,14672662,SRX3340323,SRS2641979,SRA625723,Iowa State University|Genetics Development and Cell Biology,Iowa State University,2,0.91795,0.92394,0.12634,0.12565,0.69479,0.68976,0.50879,0.5095,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-10-27,Larval,Larval,Gut,Digestive System
44036,SRR6231897,SRX3340321,SRS2641979,SRP122541,PRJNA415856,Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment,PRJNA415856,Transcriptome Analysis,Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.,,pubmed:28403821,,GFP negative cells,en GFP negative JK,,strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal non neurons|BioSampleModel:Model organism or animal,,,,,,,,,en GFP negative JK r2,en GFP negative JK r2 rev,en GFP negative JK r2 rev,The library was prepapred by the Iowa State DNA facility.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP122541,,,d7phoGFP-B_CTTGTA_R1_001.fastq.gz d7phoGFP-B_CTTGTA_R2_001.fastq.gz,fastq fastq,21627852000.0,108139260.0,d7phoGFP B CTTGTA R2 001.fastq.gz,0:100 1:100,A:5802401896;C:5026391965;G:4975450919;T:5805553498;N:18053722,100,100,,,5802401896,5026391965,4975450919,5805553498,18053722,SRX3340321,SRS2641979,SRA625723,Iowa State University|Genetics Development and Cell Biology,Iowa State University,2,0.93032,0.9242,0.11858,0.1194,0.69209,0.69544,0.50104,0.50121,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-11-02,Larval,Larval,Gut,Digestive System
45003,SRR6411472,SRX3504487,SRS2782041,SRP127390,PRJNA427283,RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA],GSE108435,Transcriptome Analysis,Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues  liver and gut.,parent bioproject:PRJNA427275,pubmed:30386173,,Gut 4 mRNA,GSM2898184,,source name:Gut|Sex:male|tissue:Gut,Gut 4 mRNA,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison.  Columns to the right of the Base Mean column represent standard DEseq2 output.  Gut 1  Gut 2  Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id  external gene name  description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers  hsapiens homolog ensembl gene  hgnc symbol  Human description and Human entrez geneid,Gut,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,Sex:male|tissue:Gut,GSM2898184,GSM2898184: Gut 4 mRNA; Danio rerio; RNA Seq,GSM2898184,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2898184,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP127390,,,Gut_2.fastq.gz,fastq,2511580170.0,49246670.0,GSM2898184 r1,0:51,A:634532680;C:591744395;G:630819200;T:654046479;N:437416,51,,,,634532680,591744395,630819200,654046479,437416,SRX3504487,SRS2782041,SRA641251,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.91491,,0.06302,,0.79632,,0.54435,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,United States,2017-12-22,Undetermined,Undetermined,Gut,Digestive System
45004,SRR6411471,SRX3504486,SRS2782040,SRP127390,PRJNA427283,RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA],GSE108435,Transcriptome Analysis,Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues  liver and gut.,parent bioproject:PRJNA427275,pubmed:30386173,,Gut 3 mRNA,GSM2898183,,source name:Gut|Sex:male|tissue:Gut,Gut 3 mRNA,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison.  Columns to the right of the Base Mean column represent standard DEseq2 output.  Gut 1  Gut 2  Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id  external gene name  description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers  hsapiens homolog ensembl gene  hgnc symbol  Human description and Human entrez geneid,Gut,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,Sex:male|tissue:Gut,GSM2898183,GSM2898183: Gut 3 mRNA; Danio rerio; RNA Seq,GSM2898183,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2898183,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP127390,,,Gut_1.fastq.gz,fastq,2336820153.0,45820003.0,GSM2898183 r1,0:51,A:592745033;C:551283776;G:583859269;T:608544280;N:387795,51,,,,592745033,551283776,583859269,608544280,387795,SRX3504486,SRS2782040,SRA641251,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,United States,2017-12-22,Undetermined,Undetermined,Gut,Digestive System
49070,SRR7641841,SRX4505270,SRS3625663,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 9dpf wt3,GSM3318287,,source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 9dpf wt3,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318287,GSM3318287: Danio rerio RNAseq intestine 9dpf wt3; Danio rerio; RNA Seq,GSM3318287,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt9dpf3_AGTCAA_R2.fastq.gz lane1_BSwt9dpf3_AGTCAA_R1.fastq.gz,fastq fastq,2761029656.0,32104996.0,GSM3318287 r1,0:43 1:43,A:708766648;C:643915678;G:711330854;T:696326829;N:689647,43,43,,,708766648,643915678,711330854,696326829,689647,SRX4505270,SRS3625663,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.89599,0.88107,0.38979,0.37161,0.72523,0.72705,0.60581,0.60845,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49071,SRR7641840,SRX4505269,SRS3625661,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 9dpf wt2,GSM3318286,,source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 9dpf wt2,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318286,GSM3318286: Danio rerio RNAseq intestine 9dpf wt2; Danio rerio; RNA Seq,GSM3318286,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt9dpf2_GGCTAC_R2.fastq.gz lane1_BSwt9dpf2_GGCTAC_R1.fastq.gz,fastq fastq,3774884086.0,43894001.0,GSM3318286 r1,0:43 1:43,A:912580559;C:950011527;G:1000247169;T:911105213;N:939618,43,43,,,912580559,950011527,1000247169,911105213,939618,SRX4505269,SRS3625661,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.91348,0.89692,0.32028,0.31,0.75479,0.76398,0.64335,0.62378,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49072,SRR7641838,SRX4505267,SRS3625659,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 9dpf wt1,GSM3318285,,source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 9dpf wt1,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318285,GSM3318285: Danio rerio RNAseq intestine 9dpf wt1; Danio rerio; RNA Seq,GSM3318285,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318285,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt9dpf1_TAGCTT_R2.fastq.gz lane1_BSwt9dpf1_TAGCTT_R1.fastq.gz,fastq fastq,2839107938.0,33012883.0,GSM3318285 r1,0:43 1:43,A:706052485;C:678593541;G:744406061;T:709347067;N:708784,43,43,,,706052485,678593541,744406061,709347067,708784,SRX4505267,SRS3625659,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.90142,0.89053,0.40928,0.39461,0.72622,0.72768,0.51721,0.5385,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49073,SRR7641837,SRX4505266,SRS3625658,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 7dpf wt3,GSM3318284,,source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 7dpf wt3,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318284,GSM3318284: Danio rerio RNAseq intestine 7dpf wt3; Danio rerio; RNA Seq,GSM3318284,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318284,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt7dpf3_GATCAG_R1.fastq.gz lane1_BSwt7dpf3_GATCAG_R2.fastq.gz,fastq fastq,3032189462.0,35258017.0,GSM3318284 r1,0:43 1:43,A:728621779;C:727851984;G:867302660;T:707649251;N:763788,43,43,,,728621779,727851984,867302660,707649251,763788,SRX4505266,SRS3625658,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.87964,0.8732,0.36258,0.35306,0.7259,0.72934,0.56793,0.56457,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49074,SRR7641836,SRX4505265,SRS3625657,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 7dpf wt2,GSM3318283,,source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 7dpf wt2,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318283,GSM3318283: Danio rerio RNAseq intestine 7dpf wt2; Danio rerio; RNA Seq,GSM3318283,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318283,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt7dpf2_ACTTGA_R2.fastq.gz lane1_BSwt7dpf2_ACTTGA_R1.fastq.gz,fastq fastq,2796267812.0,32514742.0,GSM3318283 r1,0:43 1:43,A:678627733;C:682194336;G:763077086;T:671672090;N:696567,43,43,,,678627733,682194336,763077086,671672090,696567,SRX4505265,SRS3625657,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.88818,0.88174,0.43784,0.42578,0.72531,0.72417,0.51845,0.53225,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49075,SRR7641834,SRX4505264,SRS3625656,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 7dpf wt1,GSM3318282,,source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 7dpf wt1,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318282,GSM3318282: Danio rerio RNAseq intestine 7dpf wt1; Danio rerio; RNA Seq,GSM3318282,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318282,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt7dpf1_TTAGGC_R2.fastq.gz lane1_BSwt7dpf1_TTAGGC_R1.fastq.gz,fastq fastq,2657998302.0,30906957.0,GSM3318282 r1,0:43 1:43,A:670335271;C:630669243;G:685436534;T:670905092;N:652162,43,43,,,670335271,630669243,685436534,670905092,652162,SRX4505264,SRS3625656,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.87993,0.87022,0.42578,0.40713,0.69828,0.70244,0.54254,0.55209,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49076,SRR7641833,SRX4505263,SRS3625655,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 5dpf wt3,GSM3318281,,source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 5dpf wt3,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318281,GSM3318281: Danio rerio RNAseq intestine 5dpf wt3; Danio rerio; RNA Seq,GSM3318281,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318281,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt5dpf3_CAGATC_R1.fastq.gz lane1_BSwt5dpf3_CAGATC_R2.fastq.gz,fastq fastq,3471426378.0,40365423.0,GSM3318281 r1,0:43 1:43,A:816007186;C:888388842;G:957708559;T:808447064;N:874727,43,43,,,816007186,888388842,957708559,808447064,874727,SRX4505263,SRS3625655,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.86569,0.86483,0.38669,0.37568,0.7277,0.73148,0.51986,0.52105,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49077,SRR7641832,SRX4505262,SRS3625654,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 5dpf wt2,GSM3318280,,source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 5dpf wt2,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318280,GSM3318280: Danio rerio RNAseq intestine 5dpf wt2; Danio rerio; RNA Seq,GSM3318280,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318280,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt5dpf2_GCCAAT_R2.fastq.gz lane1_BSwt5dpf2_GCCAAT_R1.fastq.gz,fastq fastq,2424100404.0,28187214.0,GSM3318280 r1,0:43 1:43,A:657799034;C:534330605;G:575770800;T:655604713;N:595252,43,43,,,657799034,534330605,575770800,655604713,595252,SRX4505262,SRS3625654,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.85487,0.83514,0.56287,0.53286,0.69583,0.69658,0.54518,0.55246,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
49078,SRR7641830,SRX4505261,SRS3625653,SRP156282,PRJNA484346,Epigenetic regulation of zebrafish intestinal development,GSE118076,Other,The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.,,,,Danio rerio RNAseq intestine 5dpf wt1,GSM3318279,,source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,Danio rerio RNAseq intestine 5dpf wt1,RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,intestine,,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.,strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a,GSM3318279,GSM3318279: Danio rerio RNAseq intestine 5dpf wt1; Danio rerio; RNA Seq,GSM3318279,,1,Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.,GEO Accession:GSM3318279,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP156282,,,lane1_BSwt5dpf1_ACAGTG_R1.fastq.gz lane1_BSwt5dpf1_ACAGTG_R2.fastq.gz,fastq fastq,2258154890.0,26257615.0,GSM3318279 r1,0:43 1:43,A:568380294;C:542047927;G:584939179;T:562222871;N:564619,43,43,,,568380294,542047927,584939179,562222871,564619,SRX4505261,SRS3625653,SRA751578,GEO,"Molecular Biology, Radboud University",2,0.89313,0.87302,0.42444,0.40784,0.72096,0.72393,0.58673,0.60423,43,43,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Netherlands,2018-08-03,Larval,Larval,Gut,Digestive System
53019,SRR9662020,SRX6422896,SRS5079686,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Intestine rep2,GSM3934888,,source name:Tissue|strain:Tuebingen|tissue:Intestine,YueLab RNA Seq Intestine rep2,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Intestine,GSM3934888,GSM3934888: YueLab RNA Seq Intestine rep2; Danio rerio; RNA Seq,GSM3934888,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934888,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Intestine-rep2_SE.fastq.gz,fastq,1692722829.0,30387989.0,GSM3934888 r1,0:55.70,A:384930576;C:443068642;G:407616609;T:444110335;N:12996667,55,,,,384930576,443068642,407616609,444110335,12996667,SRX6422896,SRS5079686,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",1,0.9407,,0.20429,,0.80071,,0.63627,,51,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Gut,Digestive System
53020,SRR9662019,SRX6422895,SRS5079685,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Intestine rep1,GSM3934887,,source name:Tissue|strain:Tuebingen|tissue:Intestine,YueLab RNA Seq Intestine rep1,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Intestine,GSM3934887,GSM3934887: YueLab RNA Seq Intestine rep1; Danio rerio; RNA Seq,GSM3934887,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934887,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Intestine-rep1_1.fastq.gz YueLab-RNA-Seq-Intestine-rep1_2.fastq.gz,fastq fastq,3793725541.0,31407590.0,GSM3934887 r1,0:60.48 1:60.31,A:996160866;C:872713802;G:866478996;T:1058315641;N:56236,60,60,,,996160866,872713802,866478996,1058315641,56236,SRX6422895,SRS5079685,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.96494,0.96816,0.10241,0.09966,0.73705,0.73992,0.53336,0.5394,61,61,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Gut,Digestive System
53594,SRR9960231,SRX6707776,SRS5261677,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs200vm,GSM4029395,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200μm PS MPs,MPs200vm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200μm PS MPs,GSM4029395,GSM4029395: MPs200vm; Danio rerio; RNA Seq,GSM4029395,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029395,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs200vm_1.fq.gz MPs200vm_2.fq.gz,fastq fastq,105309618900.0,351032063.0,GSM4029395 r1,0:150 1:150,A:27241602982;C:19773063887;G:28015499540;T:30277575281;N:1877210,150,150,,,27241602982,19773063887,28015499540,30277575281,1877210,SRX6707776,SRS5261677,SRA938912,GEO,Nanjing University,2,0.0,0.87735,0.0,0.07963,1.0,0.83049,,0.55138,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53595,SRR9960230,SRX6707775,SRS5261676,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs5vm,GSM4029394,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5μm PS MPs,MPs5vm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5μm PS MPs,GSM4029394,GSM4029394: MPs5vm; Danio rerio; RNA Seq,GSM4029394,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029394,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs5vm_1.fq.gz MPs5vm_2.fq.gz,fastq fastq,98563904100.0,328546347.0,GSM4029394 r1,0:150 1:150,A:26023907285;C:17974044830;G:25736568268;T:28827634883;N:1748834,150,150,,,26023907285,17974044830,25736568268,28827634883,1748834,SRX6707775,SRS5261676,SRA938912,GEO,Nanjing University,2,0.0,0.86592,0.0,0.09908,1.0,0.81552,,0.55476,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53596,SRR9960229,SRX6707774,SRS5261675,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs100nm,GSM4029393,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:100nm PS MPs,MPs100nm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:100nm PS MPs,GSM4029393,GSM4029393: MPs100nm; Danio rerio; RNA Seq,GSM4029393,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029393,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs100nm_1.fq.gz MPs100nm_2.fq.gz,fastq fastq,122539718400.0,408465728.0,GSM4029393 r1,0:150 1:150,A:32283417066;C:22576112318;G:30470461014;T:37207888685;N:1839317,150,150,,,32283417066,22576112318,30470461014,37207888685,1839317,SRX6707774,SRS5261675,SRA938912,GEO,Nanjing University,2,0.0,0.88187,0.0,0.09087,1.0,0.82428,,0.53597,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53597,SRR9960228,SRX6707773,SRS5261674,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,CK,GSM4029392,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:n1,CK,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:n1,GSM4029392,GSM4029392: CK; Danio rerio; RNA Seq,GSM4029392,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029392,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,CK_1.fq.gz CK_2.fq.gz,fastq fastq,111761141100.0,372537137.0,GSM4029392 r1,0:150 1:150,A:29264568248;C:21295511514;G:29897320083;T:31301732224;N:2009031,150,150,,,29264568248,21295511514,29897320083,31301732224,2009031,SRX6707773,SRS5261674,SRA938912,GEO,Nanjing University,2,0.0,0.88395,0.0,0.08593,1.0,0.80466,,0.46326,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System