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
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
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
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
55495,SRR10511896,SRX7200010,SRS5705565,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta2Gut2,GSM4187022,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2,3dpRSta2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2|age dpf = dpf,GSM4187022,GSM4187022: 3dpRSta2Gut2; Danio rerio; RNA Seq,GSM4187022,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_27_concat_R1.fastq.gz,fastq,1397453550.0,27401050.0,GSM4187022 r1,0:51 1:0,A:409993093;C:286631833;G:275766237;T:425009393;N:52994,51,0,,,409993093,286631833,275766237,425009393,52994,SRX7200010,SRS5705565,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9238,,0.127,,0.74718,,0.55171,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55496,SRR10511895,SRX7200009,SRS5705564,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta2Gut1,GSM4187021,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2,3dpRSta2Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2|age dpf = dpf,GSM4187021,GSM4187021: 3dpRSta2Gut1; Danio rerio; RNA Seq,GSM4187021,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_23_concat_R1.fastq.gz,fastq,1571369211.0,30811161.0,GSM4187021 r1,0:51 1:0,A:451585039;C:329412420;G:316009619;T:474302622;N:59511,51,0,,,451585039,329412420,316009619,474302622,59511,SRX7200009,SRS5705564,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.92047,,0.12142,,0.74785,,0.56011,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55497,SRR10511894,SRX7200008,SRS5705563,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta1Gut3,GSM4187020,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1,3dpRSta1Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1|age dpf = dpf,GSM4187020,GSM4187020: 3dpRSta1Gut3; Danio rerio; RNA Seq,GSM4187020,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_22_concat_R1.fastq.gz,fastq,1473918717.0,28900367.0,GSM4187020 r1,0:51 1:0,A:422349451;C:308266246;G:300748378;T:442499660;N:54982,51,0,,,422349451,308266246,300748378,442499660,54982,SRX7200008,SRS5705563,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93232,,0.10841,,0.7573,,0.53817,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55498,SRR10511893,SRX7200007,SRS5705562,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta1Gut1,GSM4187019,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1,3dpRSta1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1|age dpf = dpf,GSM4187019,GSM4187019: 3dpRSta1Gut1; Danio rerio; RNA Seq,GSM4187019,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_21_concat_R1.fastq.gz,fastq,1551630273.0,30424123.0,GSM4187019 r1,0:51 1:0,A:451110725;C:322314892;G:308247205;T:469898838;N:58613,51,0,,,451110725,322314892,308247205,469898838,58613,SRX7200007,SRS5705562,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9272,,0.11972,,0.75822,,0.54861,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55499,SRR10511892,SRX7200006,SRS5705561,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed2Gut3,GSM4187018,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpRFed2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187018,GSM4187018: 3dpRFed2Gut3; Danio rerio; RNA Seq,GSM4187018,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_20_concat_R1.fastq.gz,fastq,1429183557.0,28023207.0,GSM4187018 r1,0:51 1:0,A:406259184;C:299540462;G:297537630;T:425792267;N:54014,51,0,,,406259184,299540462,297537630,425792267,54014,SRX7200006,SRS5705561,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93776,,0.10446,,0.75659,,0.51357,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55500,SRR10511891,SRX7200005,SRS5705560,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed2Gut2,GSM4187017,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpRFed2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187017,GSM4187017: 3dpRFed2Gut2; Danio rerio; RNA Seq,GSM4187017,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_19_concat_R1.fastq.gz,fastq,1766365875.0,34634625.0,GSM4187017 r1,0:51 1:0,A:499095968;C:376678270;G:363861124;T:526664286;N:66227,51,0,,,499095968,376678270,363861124,526664286,66227,SRX7200005,SRS5705560,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93356,,0.10506,,0.75812,,0.54405,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55501,SRR10511882,SRX7200004,SRS5705559,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSFed1Gut3,GSM4187008,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,21dpSFed1Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187008,GSM4187008: 21dpSFed1Gut3; Danio rerio; RNA Seq,GSM4187008,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187008,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_10_concat_R1.fastq.gz,fastq,1592532834.0,31226134.0,GSM4187008 r1,0:51 1:0,A:429617322;C:351337972;G:347154272;T:464366202;N:57066,51,0,,,429617322,351337972,347154272,464366202,57066,SRX7200004,SRS5705559,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93898,,0.09149,,0.75568,,0.51578,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55502,SRR10511881,SRX7200003,SRS5705558,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSFed1Gut1,GSM4187007,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,21dpSFed1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187007,GSM4187007: 21dpSFed1Gut1; Danio rerio; RNA Seq,GSM4187007,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187007,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_9_concat_R1.fastq.gz,fastq,1575514695.0,30892445.0,GSM4187007 r1,0:51 1:0,A:441324595;C:335749891;G:331699440;T:466684268;N:56501,51,0,,,441324595,335749891,331699440,466684268,56501,SRX7200003,SRS5705558,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93304,,0.11059,,0.75286,,0.55511,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55503,SRR10511880,SRX7200002,SRS5705557,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta2Gut3,GSM4187006,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,3dpSSta2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187006,GSM4187006: 3dpSSta2Gut3; Danio rerio; RNA Seq,GSM4187006,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187006,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_8_concat_R1.fastq.gz,fastq,1785917949.0,35017999.0,GSM4187006 r1,0:51 1:0,A:509554159;C:377147211;G:365503374;T:533656366;N:56839,51,0,,,509554159,377147211,365503374,533656366,56839,SRX7200002,SRS5705557,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93641,,0.11479,,0.75351,,0.53275,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55504,SRR10511879,SRX7200001,SRS5705556,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta2Gut2,GSM4187005,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,3dpSSta2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187005,GSM4187005: 3dpSSta2Gut2; Danio rerio; RNA Seq,GSM4187005,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187005,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_7_concat_R1.fastq.gz,fastq,1789874325.0,35095575.0,GSM4187005 r1,0:51 1:0,A:495592326;C:391304311;G:373137484;T:529784276;N:55928,51,0,,,495592326,391304311,373137484,529784276,55928,SRX7200001,SRS5705556,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9421,,0.1111,,0.74566,,0.54158,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55505,SRR10511878,SRX7200000,SRS5705555,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta1Gut2,GSM4187004,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 1,3dpSSta1Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 1|age dpf = dpf,GSM4187004,GSM4187004: 3dpSSta1Gut2; Danio rerio; RNA Seq,GSM4187004,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187004,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_6_concat_R1.fastq.gz,fastq,1641362580.0,32183580.0,GSM4187004 r1,0:51 1:0,A:483646499;C:336487643;G:323951194;T:497225233;N:52011,51,0,,,483646499,336487643,323951194,497225233,52011,SRX7200000,SRS5705555,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9344,,0.13244,,0.74734,,0.52964,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55506,SRR10511877,SRX7199999,SRS5705554,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta1Gut1,GSM4187003,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 1,3dpSSta1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 1|age dpf = dpf,GSM4187003,GSM4187003: 3dpSSta1Gut1; Danio rerio; RNA Seq,GSM4187003,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187003,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_5_concat_R1.fastq.gz,fastq,1571663532.0,30816932.0,GSM4187003 r1,0:51 1:0,A:454772545;C:325458319;G:321434801;T:469947006;N:50861,51,0,,,454772545,325458319,321434801,469947006,50861,SRX7199999,SRS5705554,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93659,,0.11683,,0.75213,,0.52836,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55507,SRR10511876,SRX7199998,SRS5705553,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSFed2Gut3,GSM4187002,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpSFed2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187002,GSM4187002: 3dpSFed2Gut3; Danio rerio; RNA Seq,GSM4187002,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187002,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_4_concat_R1.fastq.gz,fastq,1561236174.0,30612474.0,GSM4187002 r1,0:51 1:0,A:467439399;C:310187678;G:304525609;T:479032805;N:50683,51,0,,,467439399,310187678,304525609,479032805,50683,SRX7199998,SRS5705553,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93358,,0.14283,,0.74939,,0.56013,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55508,SRR10511875,SRX7199997,SRS5705552,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSFed2Gut2,GSM4187001,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpSFed2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187001,GSM4187001: 3dpSFed2Gut2; Danio rerio; RNA Seq,GSM4187001,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187001,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_3_concat_R1.fastq.gz,fastq,1927545255.0,37795005.0,GSM4187001 r1,0:51 1:0,A:567770670;C:395455630;G:379200223;T:585057600;N:61132,51,0,,,567770670,395455630,379200223,585057600,61132,SRX7199997,SRS5705552,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93207,,0.13563,,0.75144,,0.54701,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55509,SRR10511890,SRX7199996,SRS5705551,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed1Gut3,GSM4187016,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,3dpRFed1Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187016,GSM4187016: 3dpRFed1Gut3; Danio rerio; RNA Seq,GSM4187016,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187016,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_18_concat_R1.fastq.gz,fastq,1733200167.0,33984317.0,GSM4187016 r1,0:51 1:0,A:478883149;C:377608593;G:368322683;T:508321013;N:64729,51,0,,,478883149,377608593,368322683,508321013,64729,SRX7199996,SRS5705551,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93695,,0.09593,,0.75341,,0.55416,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55510,SRR10511889,SRX7199995,SRS5705550,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed1Gut2,GSM4187015,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,3dpRFed1Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187015,GSM4187015: 3dpRFed1Gut2; Danio rerio; RNA Seq,GSM4187015,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187015,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_17_concat_R1.fastq.gz,fastq,1639139490.0,32139990.0,GSM4187015 r1,0:51 1:0,A:472266921;C:343820482;G:331431433;T:491557290;N:63364,51,0,,,472266921,343820482,331431433,491557290,63364,SRX7199995,SRS5705550,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.92641,,0.11798,,0.74614,,0.55037,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55511,SRR10511888,SRX7199994,SRS5705549,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSSta2Gut3,GSM4187014,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,21dpSSta2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187014,GSM4187014: 21dpSSta2Gut3; Danio rerio; RNA Seq,GSM4187014,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187014,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_28_concat_R1.fastq,fastq,1957248165.0,38377415.0,GSM4187014 r1,0:51 1:0,A:568790177;C:410992982;G:388696297;T:588697675;N:71034,51,0,,,568790177,410992982,388696297,588697675,71034,SRX7199994,SRS5705549,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.937,,0.12586,,0.75921,,0.53627,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55512,SRR10511887,SRX7199993,SRS5705548,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSSta2Gut2,GSM4187013,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,21dpSSta2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187013,GSM4187013: 21dpSSta2Gut2; Danio rerio; RNA Seq,GSM4187013,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187013,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_16_concat_R1.fastq.gz,fastq,1722397500.0,33772500.0,GSM4187013 r1,0:51 1:0,A:483227292;C:368630214;G:361368304;T:509108986;N:62704,51,0,,,483227292,368630214,361368304,509108986,62704,SRX7199993,SRS5705548,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.94065,,0.11314,,0.73726,,0.53094,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55513,SRR10511886,SRX7199992,SRS5705547,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpsSta2Gut1,GSM4187012,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,21dpsSta2Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187012,GSM4187012: 21dpsSta2Gut1; Danio rerio; RNA Seq,GSM4187012,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187012,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_15_concat_R1.fastq.gz,fastq,1883046633.0,36922483.0,GSM4187012 r1,0:51 1:0,A:535885753;C:401729105;G:382301792;T:563061958;N:68025,51,0,,,535885753,401729105,382301792,563061958,68025,SRX7199992,SRS5705547,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.94161,,0.11585,,0.74848,,0.50594,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55514,SRR10511885,SRX7199991,SRS5705546,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSSta1Gut2,GSM4187011,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 1,21dpSSta1Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 1|age dpf = dpf,GSM4187011,GSM4187011: 21dpSSta1Gut2; Danio rerio; RNA Seq,GSM4187011,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187011,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_14_concat_R1.fastq.gz,fastq,1810471950.0,35499450.0,GSM4187011 r1,0:51 1:0,A:515524495;C:386623119;G:369300060;T:538958945;N:65331,51,0,,,515524495,386623119,369300060,538958945,65331,SRX7199991,SRS5705546,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93788,,0.1201,,0.73576,,0.536,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55515,SRR10511884,SRX7199990,SRS5705545,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSFed2Gut3,GSM4187010,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,21dpSFed2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187010,GSM4187010: 21dpSFed2Gut3; Danio rerio; RNA Seq,GSM4187010,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187010,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_12_concat_R1.fastq.gz,fastq,1594835535.0,31271285.0,GSM4187010 r1,0:51 1:0,A:456360065;C:335880726;G:319279080;T:483257577;N:58087,51,0,,,456360065,335880726,319279080,483257577,58087,SRX7199990,SRS5705545,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.935,,0.11846,,0.7556,,0.54994,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55516,SRR10511883,SRX7199989,SRS5705544,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpsFed2Gut1,GSM4187009,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,21dpsFed2Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187009,GSM4187009: 21dpsFed2Gut1; Danio rerio; RNA Seq,GSM4187009,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187009,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_11_concat_R1.fastq.gz,fastq,1657780041.0,32505491.0,GSM4187009 r1,0:51 1:0,A:467924183;C:353835126;G:340667908;T:495293545;N:59279,51,0,,,467924183,353835126,340667908,495293545,59279,SRX7199989,SRS5705544,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93452,,0.1059,,0.75897,,0.56316,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
55517,SRR10511874,SRX7199988,SRS5705543,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSFed1Gut1,GSM4187000,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,3dpSFed1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated  all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt  1.5g calcium sulfate  0.75g sodium bicarbonate  10 12 drops methylene blue  10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf  embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank  with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation  feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding  we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187000,GSM4187000: 3dpSFed1Gut1; Danio rerio; RNA Seq,GSM4187000,,1,Frozen intestinal samples stored in Trizol at  80oC were homogenized using Zirconium oxide beads Biospec  11079107 and a Vortex Genie2 Scientific Industries  1311 V fitted with a Vortex Adapter Scientific Industries  13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating.  Following homogenization  a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube  to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation  samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher  12185010 and the PureLink RNA Mini kit Thermo Fisher  12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at  80oC 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 50bp single end read according to the manufacturer's instructions. Prior to library preparation  RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187000,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_1_concat_R1.fastq.gz,fastq,1579970973.0,30979823.0,GSM4187000 r1,0:51 1:0,A:438395339;C:340541415;G:338487129;T:462497338;N:49752,51,0,,,438395339,340541415,338487129,462497338,49752,SRX7199988,SRS5705543,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.94225,,0.09616,,0.76021,,0.53717,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System
59456,SRR11917488,SRX8463993,SRS6765214,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV3 IEC,GSM4588952,,tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells,CV3 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Other intestinal epithelium cells,GSM4588952,GSM4588952: CV3 IEC; Danio rerio; RNA Seq,GSM4588952,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588952,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S12_S12_L006_R1_001.fastq.gz,fastq,989770770.0,19407270.0,GSM4588952 r1,0:51 1:0,A:281534917;C:214882196;G:215847745;T:277443986;N:61926,51,0,,,281534917,214882196,215847745,277443986,61926,SRX8463993,SRS6765214,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.85529,,0.16671,,0.87886,,0.67632,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59457,SRR11917489,SRX8463993,SRS6765214,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV3 IEC,GSM4588952,,tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells,CV3 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Other intestinal epithelium cells,GSM4588952,GSM4588952: CV3 IEC; Danio rerio; RNA Seq,GSM4588952,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588952,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S12_S12_L007_R1_001.fastq.gz,fastq,970629807.0,19031957.0,GSM4588952 r2,0:51 1:0,A:276238559;C:210614378;G:211564800;T:272166193;N:45877,51,0,,,276238559,210614378,211564800,272166193,45877,SRX8463993,SRS6765214,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.85557,,0.16793,,0.87819,,0.68247,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59458,SRR11917486,SRX8463992,SRS6765213,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV3 EEC,GSM4588951,,tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells,CV3 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Enteroendocrine cells,GSM4588951,GSM4588951: CV3 EEC; Danio rerio; RNA Seq,GSM4588951,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588951,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S11_S11_L006_R1_001.fastq.gz,fastq,1116941667.0,21900817.0,GSM4588951 r1,0:51 1:0,A:320236417;C:240301779;G:240594328;T:315739633;N:69510,51,0,,,320236417,240301779,240594328,315739633,69510,SRX8463992,SRS6765213,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.60354,,0.13851,,0.86699,,0.49869,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59459,SRR11917487,SRX8463992,SRS6765213,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV3 EEC,GSM4588951,,tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells,CV3 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Enteroendocrine cells,GSM4588951,GSM4588951: CV3 EEC; Danio rerio; RNA Seq,GSM4588951,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588951,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S11_S11_L007_R1_001.fastq.gz,fastq,1100752584.0,21583384.0,GSM4588951 r2,0:51 1:0,A:315761089;C:236724849;G:236992907;T:311222165;N:51574,51,0,,,315761089,236724849,236992907,311222165,51574,SRX8463992,SRS6765213,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.60449,,0.13991,,0.86519,,0.49824,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59460,SRR11917484,SRX8463991,SRS6765212,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF3 IEC,GSM4588950,,tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells,GF3 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Other intestinal epithelium cells,GSM4588950,GSM4588950: GF3 IEC; Danio rerio; RNA Seq,GSM4588950,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588950,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S10_S10_L006_R1_001.fastq.gz,fastq,1158251565.0,22710815.0,GSM4588950 r1,0:51 1:0,A:329413690;C:252108273;G:252469757;T:324185740;N:74105,51,0,,,329413690,252108273,252469757,324185740,74105,SRX8463991,SRS6765212,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.8667,,0.17916,,0.81631,,0.60631,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59461,SRR11917485,SRX8463991,SRS6765212,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF3 IEC,GSM4588950,,tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells,GF3 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Other intestinal epithelium cells,GSM4588950,GSM4588950: GF3 IEC; Danio rerio; RNA Seq,GSM4588950,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588950,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S10_S10_L007_R1_001.fastq.gz,fastq,1140502902.0,22362802.0,GSM4588950 r2,0:51 1:0,A:324550812;C:248145888;G:248413979;T:319338762;N:53461,51,0,,,324550812,248145888,248413979,319338762,53461,SRX8463991,SRS6765212,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.86472,,0.17957,,0.81604,,0.60323,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59462,SRR11917482,SRX8463990,SRS6765211,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF3 EEC,GSM4588949,,tissue:intestine|group:Germ free|cell type:Enteroendocrine cells,GF3 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Enteroendocrine cells,GSM4588949,GSM4588949: GF3 EEC; Danio rerio; RNA Seq,GSM4588949,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S9_S9_L006_R1_001.fastq.gz,fastq,1124335902.0,22045802.0,GSM4588949 r1,0:51 1:0,A:323779238;C:243076994;G:243426022;T:313982480;N:71168,51,0,,,323779238,243076994,243426022,313982480,71168,SRX8463990,SRS6765211,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.82417,,0.22133,,0.82262,,0.53921,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59463,SRR11917483,SRX8463990,SRS6765211,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF3 EEC,GSM4588949,,tissue:intestine|group:Germ free|cell type:Enteroendocrine cells,GF3 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Enteroendocrine cells,GSM4588949,GSM4588949: GF3 EEC; Danio rerio; RNA Seq,GSM4588949,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S9_S9_L007_R1_001.fastq.gz,fastq,1102409217.0,21615867.0,GSM4588949 r2,0:51 1:0,A:317592665;C:238208950;G:238561212;T:307994643;N:51747,51,0,,,317592665,238208950,238561212,307994643,51747,SRX8463990,SRS6765211,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.82287,,0.22204,,0.82037,,0.54199,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59464,SRR11917480,SRX8463989,SRS6765210,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV2 IED,GSM4588948,,tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells,CV2 IED,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Other intestinal epithelium cells,GSM4588948,GSM4588948: CV2 IED; Danio rerio; RNA Seq,GSM4588948,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588948,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S8_S8_L006_R1_001.fastq.gz,fastq,1153200474.0,22611774.0,GSM4588948 r1,0:51 1:0,A:325960158;C:253028514;G:253402635;T:320734834;N:74333,51,0,,,325960158,253028514,253402635,320734834,74333,SRX8463989,SRS6765210,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.87013,,0.18232,,0.74217,,0.52659,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59465,SRR11917481,SRX8463989,SRS6765210,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV2 IED,GSM4588948,,tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells,CV2 IED,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Other intestinal epithelium cells,GSM4588948,GSM4588948: CV2 IED; Danio rerio; RNA Seq,GSM4588948,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588948,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S8_S8_L007_R1_001.fastq.gz,fastq,1129915098.0,22155198.0,GSM4588948 r2,0:51 1:0,A:319498713;C:247882461;G:248181774;T:314298474;N:53676,51,0,,,319498713,247882461,248181774,314298474,53676,SRX8463989,SRS6765210,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.8695,,0.18113,,0.74156,,0.52983,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59466,SRR11917478,SRX8463988,SRS6765209,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV2 EEC,GSM4588947,,tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells,CV2 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Enteroendocrine cells,GSM4588947,GSM4588947: CV2 EEC; Danio rerio; RNA Seq,GSM4588947,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588947,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S7_S7_L006_R1_001.fastq.gz,fastq,1378636692.0,27032092.0,GSM4588947 r1,0:51 1:0,A:391264014;C:300388051;G:302055880;T:384841320;N:87427,51,0,,,391264014,300388051,302055880,384841320,87427,SRX8463988,SRS6765209,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.86069,,0.20189,,0.74643,,0.48529,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59467,SRR11917479,SRX8463988,SRS6765209,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV2 EEC,GSM4588947,,tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells,CV2 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Enteroendocrine cells,GSM4588947,GSM4588947: CV2 EEC; Danio rerio; RNA Seq,GSM4588947,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588947,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S7_S7_L007_R1_001.fastq.gz,fastq,1355490597.0,26578247.0,GSM4588947 r2,0:51 1:0,A:384933467;C:295204222;G:296869394;T:378419448;N:64066,51,0,,,384933467,295204222,296869394,378419448,64066,SRX8463988,SRS6765209,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.86045,,0.20313,,0.74667,,0.48228,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59468,SRR11917476,SRX8463987,SRS6765208,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF2 IEC,GSM4588946,,tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells,GF2 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Other intestinal epithelium cells,GSM4588946,GSM4588946: GF2 IEC; Danio rerio; RNA Seq,GSM4588946,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588946,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S6_S6_L006_R1_001.fastq.gz,fastq,1096567014.0,21501314.0,GSM4588946 r1,0:51 1:0,A:310133103;C:241356167;G:241726971;T:303281850;N:68923,51,0,,,310133103,241356167,241726971,303281850,68923,SRX8463987,SRS6765208,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.87328,,0.17387,,0.86657,,0.64049,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59469,SRR11917477,SRX8463987,SRS6765208,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF2 IEC,GSM4588946,,tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells,GF2 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Other intestinal epithelium cells,GSM4588946,GSM4588946: GF2 IEC; Danio rerio; RNA Seq,GSM4588946,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588946,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S6_S6_L007_R1_001.fastq.gz,fastq,1077795036.0,21133236.0,GSM4588946 r2,0:51 1:0,A:305006168;C:237104899;G:237493375;T:298139724;N:50870,51,0,,,305006168,237104899,237493375,298139724,50870,SRX8463987,SRS6765208,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.87121,,0.17225,,0.86776,,0.65328,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59470,SRR11917474,SRX8463986,SRS6765207,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF2 EEC,GSM4588945,,tissue:intestine|group:Germ free|cell type:Enteroendocrine cells,GF2 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Enteroendocrine cells,GSM4588945,GSM4588945: GF2 EEC; Danio rerio; RNA Seq,GSM4588945,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588945,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S5_S5_L006_R1_001.fastq.gz,fastq,993591180.0,19482180.0,GSM4588945 r1,0:51 1:0,A:282890765;C:216703865;G:217669683;T:276263863;N:63004,51,0,,,282890765,216703865,217669683,276263863,63004,SRX8463986,SRS6765207,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.84026,,0.15974,,0.84542,,0.62819,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59471,SRR11917475,SRX8463986,SRS6765207,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF2 EEC,GSM4588945,,tissue:intestine|group:Germ free|cell type:Enteroendocrine cells,GF2 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Enteroendocrine cells,GSM4588945,GSM4588945: GF2 EEC; Danio rerio; RNA Seq,GSM4588945,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588945,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S5_S5_L007_R1_001.fastq.gz,fastq,974360049.0,19105099.0,GSM4588945 r2,0:51 1:0,A:277539322;C:212402095;G:213358281;T:271014144;N:46207,51,0,,,277539322,212402095,213358281,271014144,46207,SRX8463986,SRS6765207,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.84253,,0.16032,,0.84723,,0.62874,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59472,SRR11917472,SRX8463985,SRS6765206,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV1 IEC,GSM4588944,,tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells,CV1 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Other intestinal epithelium cells,GSM4588944,GSM4588944: CV1 IEC; Danio rerio; RNA Seq,GSM4588944,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588944,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S4_S4_L006_R1_001.fastq.gz,fastq,1125747633.0,22073483.0,GSM4588944 r1,0:51 1:0,A:318281873;C:249238273;G:249957107;T:308199627;N:70753,51,0,,,318281873,249238273,249957107,308199627,70753,SRX8463985,SRS6765206,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.89074,,0.12353,,0.82816,,0.68204,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59473,SRR11917473,SRX8463985,SRS6765206,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV1 IEC,GSM4588944,,tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells,CV1 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Other intestinal epithelium cells,GSM4588944,GSM4588944: CV1 IEC; Danio rerio; RNA Seq,GSM4588944,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588944,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S4_S4_L007_R1_001.fastq.gz,fastq,1105934796.0,21684996.0,GSM4588944 r2,0:51 1:0,A:312851469;C:244757781;G:245446410;T:302827147;N:51989,51,0,,,312851469,244757781,245446410,302827147,51989,SRX8463985,SRS6765206,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.88843,,0.12342,,0.82873,,0.67656,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59474,SRR11917470,SRX8463984,SRS6765204,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV1 EEC,GSM4588943,,tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells,CV1 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Enteroendocrine cells,GSM4588943,GSM4588943: CV1 EEC; Danio rerio; RNA Seq,GSM4588943,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588943,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S3_S3_L006_R1_001.fastq.gz,fastq,942559764.0,18481564.0,GSM4588943 r1,0:51 1:0,A:263978139;C:208960440;G:211142234;T:258419586;N:59365,51,0,,,263978139,208960440,211142234,258419586,59365,SRX8463984,SRS6765204,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.84651,,0.13502,,0.87334,,0.60719,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59475,SRR11917471,SRX8463984,SRS6765204,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,CV1 EEC,GSM4588943,,tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells,CV1 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Conventionalized|cell type:Enteroendocrine cells,GSM4588943,GSM4588943: CV1 EEC; Danio rerio; RNA Seq,GSM4588943,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588943,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S3_S3_L007_R1_001.fastq.gz,fastq,923680839.0,18111389.0,GSM4588943 r2,0:51 1:0,A:258844956;C:204695214;G:206849563;T:253247421;N:43685,51,0,,,258844956,204695214,206849563,253247421,43685,SRX8463984,SRS6765204,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.84566,,0.13508,,0.8746,,0.60113,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59476,SRR11917468,SRX8463983,SRS6765205,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF1 IEC,GSM4588942,,tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells,GF1 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Other intestinal epithelium cells,GSM4588942,GSM4588942: GF1 IEC; Danio rerio; RNA Seq,GSM4588942,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588942,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S2_S2_L006_R1_001.fastq.gz,fastq,1238473698.0,24283798.0,GSM4588942 r1,0:51 1:0,A:341609725;C:281085121;G:281016378;T:334683690;N:78784,51,0,,,341609725,281085121,281016378,334683690,78784,SRX8463983,SRS6765205,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.88819,,0.1308,,0.81357,,0.57234,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59477,SRR11917469,SRX8463983,SRS6765205,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF1 IEC,GSM4588942,,tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells,GF1 IEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Other intestinal epithelium cells,GSM4588942,GSM4588942: GF1 IEC; Danio rerio; RNA Seq,GSM4588942,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588942,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S2_S2_L007_R1_001.fastq.gz,fastq,1215535785.0,23834035.0,GSM4588942 r2,0:51 1:0,A:335462084;C:275714789;G:275686585;T:328614149;N:58178,51,0,,,335462084,275714789,275686585,328614149,58178,SRX8463983,SRS6765205,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.88988,,0.13024,,0.81262,,0.57631,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59478,SRR11917466,SRX8463982,SRS6765203,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF1 EEC,GSM4588941,,tissue:intestine|group:Germ free|cell type:Enteroendocrine cells,GF1 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Enteroendocrine cells,GSM4588941,GSM4588941: GF1 EEC; Danio rerio; RNA Seq,GSM4588941,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588941,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S1_S1_L006_R1_001.fastq.gz,fastq,1106448264.0,21695064.0,GSM4588941 r1,0:51 1:0,A:312177906;C:243246164;G:244584142;T:306370900;N:69152,51,0,,,312177906,243246164,244584142,306370900,69152,SRX8463982,SRS6765203,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.7883,,0.14389,,0.88158,,0.55008,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
59479,SRR11917467,SRX8463982,SRS6765203,SRP265808,PRJNA637035,Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways,GSE151711,Transcriptome Analysis,RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.,,pubmed:38577841,,GF1 EEC,GSM4588941,,tissue:intestine|group:Germ free|cell type:Enteroendocrine cells,GF1 EEC,Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample,intestine,no treatment,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,Gnotobiotic zebrafish,group:Germ free|cell type:Enteroendocrine cells,GSM4588941,GSM4588941: GF1 EEC; Danio rerio; RNA Seq,GSM4588941,,1,Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA.  mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4588941,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP265808,,,LY-S1_S1_L007_R1_001.fastq.gz,fastq,1082299917.0,21221567.0,GSM4588941 r2,0:51 1:0,A:305489640;C:237873171;G:239135258;T:299751004;N:50844,51,0,,,305489640,237873171,239135258,299751004,50844,SRX8463982,SRS6765203,SRA1082774,GEO,"Rawls lab, MGM Department, Duke University",1,0.78533,,0.14463,,0.88229,,0.56056,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2020-06-03,Undetermined,Larval,Gut,Digestive System
63076,SRR13593802,SRX9988314,SRS8159459,SRP304042,PRJNA698416,Inhibition of goblet cell differentiation in hypothyroidism is associated with deregulated Fgf19 Fgfr4 signaling,PRJNA698416,Other,To understand the effect of thyroid hormone,,,,ablated sample rep 3,AB3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:adult|dev stage:not applicable|sex:male|tissue:Gut 5|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerion gut RNA seq,ablated sample rep 3,ablated sample rep 3,RNA sequencing for danio rerion gut,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP304042,,,Einat_ablated_gut_3_R1.fastq,fastq,2708875907.0,36368726.0,Einat ablated gut 3 R1.fastq,0:74.48 1:0,A:680087223;C:639287055;G:617080190;T:772291613;N:129826,74,0,,,680087223,639287055,617080190,772291613,129826,SRX9988314,SRS8159459,SRA1189900,Bar Ilan University|life science,Bar Ilan University,1,0.95093,,0.05335,,0.80967,,0.52613,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2021-02-01,Adult,Adult,Gut,Digestive System
63077,SRR13593803,SRX9988313,SRS8159457,SRP304042,PRJNA698416,Inhibition of goblet cell differentiation in hypothyroidism is associated with deregulated Fgf19 Fgfr4 signaling,PRJNA698416,Other,To understand the effect of thyroid hormone,,,,ablated sample rep 2,AB2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:adult|dev stage:not applicable|sex:male|tissue:Gut 4|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerion gut RNA seq,ablated sample rep 2,ablated sample rep 2,RNA sequencing for danio rerion gut,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP304042,,,Einat_ablated_gut_2_R1.fastq,fastq,2024290491.0,27170588.0,Einat ablated gut 2 R1.fastq,0:74.50 1:0,A:524899839;C:467419534;G:447383995;T:584519384;N:67739,74,0,,,524899839,467419534,447383995,584519384,67739,SRX9988313,SRS8159457,SRA1189900,Bar Ilan University|life science,Bar Ilan University,1,0.94537,,0.06614,,0.8087,,0.52796,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2021-02-01,Adult,Adult,Gut,Digestive System
63078,SRR13593804,SRX9988312,SRS8159455,SRP304042,PRJNA698416,Inhibition of goblet cell differentiation in hypothyroidism is associated with deregulated Fgf19 Fgfr4 signaling,PRJNA698416,Other,To understand the effect of thyroid hormone,,,,ablated sample rep 1,AB1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:adult|dev stage:not applicable|sex:male|tissue:Gut 3|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerion gut RNA seq,ablated sample rep 1,ablated sample rep 1,RNA sequencing for danio rerion gut,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP304042,,,Einat_ablated_gut_1_R1.fastq,fastq,1461927106.0,19623609.0,Einat ablated gut 1 R1.fastq,0:74.50 1:0,A:375794289;C:337051794;G:327941493;T:421098302;N:41228,74,0,,,375794289,337051794,327941493,421098302,41228,SRX9988312,SRS8159455,SRA1189900,Bar Ilan University|life science,Bar Ilan University,1,0.94378,,0.05467,,0.81895,,0.49133,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2021-02-01,Adult,Adult,Gut,Digestive System
63079,SRR13593805,SRX9988311,SRS8159458,SRP304042,PRJNA698416,Inhibition of goblet cell differentiation in hypothyroidism is associated with deregulated Fgf19 Fgfr4 signaling,PRJNA698416,Other,To understand the effect of thyroid hormone,,,,Control sample rep 2,CS2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:adult|dev stage:not applicable|sex:male|tissue:Gut 2|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerion gut RNA seq,Control sample rep 2,Control sample rep 2,RNA sequencing for danio rerion gut,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP304042,,,Einat_control_gut_2_R1.fastq,fastq,1541134836.0,20684259.0,Einat control gut 2 R1.fastq,0:74.51 1:0,A:387937126;C:363944491;G:348612093;T:440600639;N:40487,74,0,,,387937126,363944491,348612093,440600639,40487,SRX9988311,SRS8159458,SRA1189900,Bar Ilan University|life science,Bar Ilan University,1,0.94793,,0.0608,,0.80476,,0.52377,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2021-02-01,Adult,Adult,Gut,Digestive System
63080,SRR13593806,SRX9988310,SRS8159456,SRP304042,PRJNA698416,Inhibition of goblet cell differentiation in hypothyroidism is associated with deregulated Fgf19 Fgfr4 signaling,PRJNA698416,Other,To understand the effect of thyroid hormone,,,,Control sample rep 1,CS1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:adult|dev stage:not applicable|sex:male|tissue:Gut 1|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerion gut RNA seq,Control sample rep 1,Control sample rep 1,RNA sequencing for danio rerion gut,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP304042,,,Einat_control_gut_1_R1.fastq,fastq,1538665984.0,20648801.0,Einat control gut 1 R1.fastq,0:74.52 1:0,A:381368703;C:366635633;G:353200844;T:437407142;N:53662,74,0,,,381368703,366635633,353200844,437407142,53662,SRX9988310,SRS8159456,SRA1189900,Bar Ilan University|life science,Bar Ilan University,1,0.9476,,0.05307,,0.81134,,0.54676,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2021-02-01,Adult,Adult,Gut,Digestive System
63810,SRR14060980,SRX10435564,SRS8569035,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Torpor+radiation [18 24 M2 RAD],GSM5208645,,tissue:Gastrointestinal tract,Torpor+radiation [18 24 M2 RAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:32.64|temperature °c:18.5|melatonin µm:24,GSM5208645,GSM5208645: Torpor+radiation [18 24 M2 RAD]; Danio rerio; RNA Seq,GSM5208645,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208645,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,18-24-M2-RAD_GTGAAA_S103_L008_R1_001.fastq.gz,fastq,1589596300.0,31791926.0,GSM5208645 r1,0:50,A:343218732;C:412078303;G:480421414;T:353581599;N:296252,50,,,,343218732,412078303,480421414,353581599,296252,SRX10435564,SRS8569035,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.61709,,0.13219,,0.8379,,0.67633,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63811,SRR14060979,SRX10435563,SRS8569036,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Torpor+radiation [18 24 M1 RAD],GSM5208644,,tissue:Gastrointestinal tract,Torpor+radiation [18 24 M1 RAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:32.64|temperature °c:18.5|melatonin µm:24,GSM5208644,GSM5208644: Torpor+radiation [18 24 M1 RAD]; Danio rerio; RNA Seq,GSM5208644,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208644,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,18-24-M1-RAD_GTCCGC_S102_L008_R1_001.fastq.gz,fastq,1826597250.0,36531945.0,GSM5208644 r1,0:50,A:400114581;C:473398494;G:532511254;T:420225243;N:347678,50,,,,400114581,473398494,532511254,420225243,347678,SRX10435563,SRS8569036,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.58111,,0.13543,,0.86419,,0.68781,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63812,SRR14060978,SRX10435562,SRS8569034,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Torpor+radiation [18 24 F2 RAD],GSM5208643,,tissue:Gastrointestinal tract,Torpor+radiation [18 24 F2 RAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:32.64|temperature °c:18.5|melatonin µm:24,GSM5208643,GSM5208643: Torpor+radiation [18 24 F2 RAD]; Danio rerio; RNA Seq,GSM5208643,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208643,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,18-24-F2-RAD_GTTTCG_S101_L008_R1_001.fastq.gz,fastq,2006121600.0,40122432.0,GSM5208643 r1,0:50,A:418454946;C:561035530;G:571770538;T:454478879;N:381707,50,,,,418454946,561035530,571770538,454478879,381707,SRX10435562,SRS8569034,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.76053,,0.17325,,0.83954,,0.64698,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63813,SRR14060977,SRX10435561,SRS8569033,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Torpor+radiation [18 24 F1 RAD],GSM5208642,,tissue:Gastrointestinal tract,Torpor+radiation [18 24 F1 RAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:32.64|temperature °c:18.5|melatonin µm:24,GSM5208642,GSM5208642: Torpor+radiation [18 24 F1 RAD]; Danio rerio; RNA Seq,GSM5208642,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208642,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,18-24-F1-RAD_GTGGCC_S100_L008_R1_001.fastq.gz,fastq,2369508350.0,47390167.0,GSM5208642 r1,0:50,A:509515197;C:623307582;G:694019366;T:542224292;N:441913,50,,,,509515197,623307582,694019366,542224292,441913,SRX10435561,SRS8569033,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.62827,,0.14038,,0.828,,0.66975,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63814,SRR14060976,SRX10435560,SRS8569032,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Radiation [C M1 RAD],GSM5208641,,tissue:Gastrointestinal tract,Radiation [C M1 RAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:32.64|temperature °c:28.5|melatonin µm:0,GSM5208641,GSM5208641: Radiation [C M1 RAD]; Danio rerio; RNA Seq,GSM5208641,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208641,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,C-M1-RAD_GATCAG_S111_L008_R1_001.fastq.gz,fastq,599190900.0,11983818.0,GSM5208641 r1,0:50,A:136269333;C:152654300;G:156807839;T:153346367;N:113061,50,,,,136269333,152654300,156807839,153346367,113061,SRX10435560,SRS8569032,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.77484,,0.14395,,0.78405,,0.5761,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63815,SRR14060975,SRX10435559,SRS8569031,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Radiation [C F7 RAD],GSM5208640,,tissue:Gastrointestinal tract,Radiation [C F7 RAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:32.64|temperature °c:28.5|melatonin µm:0,GSM5208640,GSM5208640: Radiation [C F7 RAD]; Danio rerio; RNA Seq,GSM5208640,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208640,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,C-F7-RAD_TAGCTT_S110_L008_R1_001.fastq.gz,fastq,1820356400.0,36407128.0,GSM5208640 r1,0:50,A:396601070;C:476853550;G:517846835;T:428710396;N:344549,50,,,,396601070,476853550,517846835,428710396,344549,SRX10435559,SRS8569031,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.71064,,0.16141,,0.81544,,0.63869,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63816,SRR14060974,SRX10435558,SRS8569030,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Radiation [C F2 RAD],GSM5208639,,tissue:Gastrointestinal tract,Radiation [C F2 RAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:32.64|temperature °c:28.5|melatonin µm:0,GSM5208639,GSM5208639: Radiation [C F2 RAD]; Danio rerio; RNA Seq,GSM5208639,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208639,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,C-F2-RAD_GGCTAC_S107_L008_R1_001.fastq.gz,fastq,1227644200.0,24552884.0,GSM5208639 r1,0:50,A:270072562;C:315451890;G:350204178;T:291687838;N:227732,50,,,,270072562,315451890,350204178,291687838,227732,SRX10435558,SRS8569030,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.70512,,0.15321,,0.81491,,0.65123,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63819,SRR14060971,SRX10435555,SRS8569026,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Control [C F7 NORAD],GSM5208636,,tissue:Gastrointestinal tract,Control [C F7 NORAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:0|temperature °c:28.5|melatonin µm:0,GSM5208636,GSM5208636: Control [C F7 NORAD]; Danio rerio; RNA Seq,GSM5208636,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208636,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,C-F7-NORAD_CTTGTA_S109_L008_R1_001.fastq.gz,fastq,1433736900.0,28674738.0,GSM5208636 r1,0:50,A:320793907;C:370334561;G:393244317;T:349086384;N:277731,50,,,,320793907,370334561,393244317,349086384,277731,SRX10435555,SRS8569026,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.74343,,0.14223,,0.8322,,0.411,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63820,SRR14060970,SRX10435554,SRS8569028,SRP311962,PRJNA716978,Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model,GSE169522,Transcriptome Analysis,We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation,,pubmed:33920039,,Control [C F3 NORAD],GSM5208635,,tissue:Gastrointestinal tract,Control [C F3 NORAD],Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output,Gastrointestinal tract,A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,,radiation cgy:0|temperature °c:28.5|melatonin µm:0,GSM5208635,GSM5208635: Control [C F3 NORAD]; Danio rerio; RNA Seq,GSM5208635,,1,Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.,GEO Accession:GSM5208635,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP311962,,loader:fastq load.py,C-F3-NORAD_AGTCAA_S108_L008_R1_001.fastq.gz,fastq,1341408250.0,26828165.0,GSM5208635 r1,0:50,A:293343570;C:349728046;G:383602727;T:314473091;N:260816,50,,,,293343570,349728046,383602727,314473091,260816,SRX10435554,SRS8569028,SRA1209926,GEO,"Hardiman Lab, Institute for Global Food Security, Queen's University Belfast",1,0.70261,,0.14107,,0.81791,,0.57017,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2021-03-24,Undetermined,Undetermined,Gut,Digestive System
63875,SRR14163088,SRX10531558,SRS8654919,SRP313793,PRJNA720320,Quantitative Analysis of Transcriptomes of Control and BP 3 exposure embryos zebrafish by RNA sequencing,GSE171619,Transcriptome Analysis,Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without xxx 3BP 3 at the transcriptome level and find the underlying mechanism how could BP 3 impede the development of enteric nervous system. Methods:  Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos were generated by paired end sequencing  in triplicate  using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis GSEA comparing WT and BP 3 exposure groups was performed by GSEA software version 4.0.03. A nominal p value < 0.05 and false discovery rate FDR q value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. RNA seq data confirmed 159 up regulated and 73 down regulated genes in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP 3 exposure zebrafish intestinal transcriptomes  with biologic replicates  generated by RNA sequencing technology. Our results showed that 159 genes were up regulated and 73 were down regulated  in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Overall design: Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos,,,,WT 3,GSM5229431,,source name:Intestinal|strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control,WT 3,Illumina HiSeqTM 2500 used for basecalling. specific steps were followed using the methods previously described WEI L  CAO L  MIAO Y  et al. Transcriptome analysis of Spodoptera frugiperda 9 Sf9 cells infected with baculovirus  AcMNPV or AcMNPV BmK IT [J]. Biotechnol Lett  2017  398: 1129 39. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Genome build: mm9 Supplementary files format and content: tab delimited text files include MEAN TPM values for each Sample,Intestinal,Embryos of BP 3 exposure group were incubated in 2mg/L BP 3,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer’s instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control,GSM5229431,GSM5229431: WT 3; Danio rerio; RNA Seq,GSM5229431,,1,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer's instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5229431,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP313793,,loader:fastq load.py,WT_3.raw_1.fastq.gz,fastq,2953639350.0,19690929.0,GSM5229431 r1,0:150,A:817498622;C:675376889;G:684270756;T:776482401;N:10682,150,,,,817498622,675376889,684270756,776482401,10682,SRX10531558,SRS8654919,SRA1215917,GEO,"Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology",1,0.94256,,0.1225,,0.64885,,0.46986,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-04-07,Larval,Larval,Gut,Digestive System
63876,SRR14163087,SRX10531557,SRS8654918,SRP313793,PRJNA720320,Quantitative Analysis of Transcriptomes of Control and BP 3 exposure embryos zebrafish by RNA sequencing,GSE171619,Transcriptome Analysis,Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without xxx 3BP 3 at the transcriptome level and find the underlying mechanism how could BP 3 impede the development of enteric nervous system. Methods:  Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos were generated by paired end sequencing  in triplicate  using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis GSEA comparing WT and BP 3 exposure groups was performed by GSEA software version 4.0.03. A nominal p value < 0.05 and false discovery rate FDR q value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. RNA seq data confirmed 159 up regulated and 73 down regulated genes in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP 3 exposure zebrafish intestinal transcriptomes  with biologic replicates  generated by RNA sequencing technology. Our results showed that 159 genes were up regulated and 73 were down regulated  in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Overall design: Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos,,,,WT 2,GSM5229430,,source name:Intestinal|strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control,WT 2,Illumina HiSeqTM 2500 used for basecalling. specific steps were followed using the methods previously described WEI L  CAO L  MIAO Y  et al. Transcriptome analysis of Spodoptera frugiperda 9 Sf9 cells infected with baculovirus  AcMNPV or AcMNPV BmK IT [J]. Biotechnol Lett  2017  398: 1129 39. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Genome build: mm9 Supplementary files format and content: tab delimited text files include MEAN TPM values for each Sample,Intestinal,Embryos of BP 3 exposure group were incubated in 2mg/L BP 3,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer’s instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control,GSM5229430,GSM5229430: WT 2; Danio rerio; RNA Seq,GSM5229430,,1,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer's instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5229430,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP313793,,loader:fastq load.py,WT_2.raw_1.fastq.gz,fastq,3267964200.0,21786428.0,GSM5229430 r1,0:150,A:877045346;C:766610315;G:777309998;T:846989731;N:8810,150,,,,877045346,766610315,777309998,846989731,8810,SRX10531557,SRS8654918,SRA1215917,GEO,"Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology",1,0.95201,,0.09898,,0.65064,,0.47213,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-04-07,Larval,Larval,Gut,Digestive System
63877,SRR14163086,SRX10531556,SRS8654917,SRP313793,PRJNA720320,Quantitative Analysis of Transcriptomes of Control and BP 3 exposure embryos zebrafish by RNA sequencing,GSE171619,Transcriptome Analysis,Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without xxx 3BP 3 at the transcriptome level and find the underlying mechanism how could BP 3 impede the development of enteric nervous system. Methods:  Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos were generated by paired end sequencing  in triplicate  using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis GSEA comparing WT and BP 3 exposure groups was performed by GSEA software version 4.0.03. A nominal p value < 0.05 and false discovery rate FDR q value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. RNA seq data confirmed 159 up regulated and 73 down regulated genes in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP 3 exposure zebrafish intestinal transcriptomes  with biologic replicates  generated by RNA sequencing technology. Our results showed that 159 genes were up regulated and 73 were down regulated  in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Overall design: Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos,,,,WT 1,GSM5229429,,source name:Intestinal|strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control,WT 1,Illumina HiSeqTM 2500 used for basecalling. specific steps were followed using the methods previously described WEI L  CAO L  MIAO Y  et al. Transcriptome analysis of Spodoptera frugiperda 9 Sf9 cells infected with baculovirus  AcMNPV or AcMNPV BmK IT [J]. Biotechnol Lett  2017  398: 1129 39. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Genome build: mm9 Supplementary files format and content: tab delimited text files include MEAN TPM values for each Sample,Intestinal,Embryos of BP 3 exposure group were incubated in 2mg/L BP 3,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer’s instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control,GSM5229429,GSM5229429: WT 1; Danio rerio; RNA Seq,GSM5229429,,1,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer's instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5229429,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP313793,,loader:fastq load.py,WT_1.raw_1.fastq.gz,fastq,4168065900.0,27787106.0,GSM5229429 r1,0:150,A:1120621692;C:971245010;G:991822128;T:1084366148;N:10922,150,,,,1120621692,971245010,991822128,1084366148,10922,SRX10531556,SRS8654917,SRA1215917,GEO,"Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology",1,0.95088,,0.10223,,0.64932,,0.47628,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-04-07,Larval,Larval,Gut,Digestive System
63878,SRR14163085,SRX10531555,SRS8654916,SRP313793,PRJNA720320,Quantitative Analysis of Transcriptomes of Control and BP 3 exposure embryos zebrafish by RNA sequencing,GSE171619,Transcriptome Analysis,Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without xxx 3BP 3 at the transcriptome level and find the underlying mechanism how could BP 3 impede the development of enteric nervous system. Methods:  Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos were generated by paired end sequencing  in triplicate  using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis GSEA comparing WT and BP 3 exposure groups was performed by GSEA software version 4.0.03. A nominal p value < 0.05 and false discovery rate FDR q value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. RNA seq data confirmed 159 up regulated and 73 down regulated genes in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP 3 exposure zebrafish intestinal transcriptomes  with biologic replicates  generated by RNA sequencing technology. Our results showed that 159 genes were up regulated and 73 were down regulated  in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Overall design: Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos,,,,BP 3 3,GSM5229428,,source name:Intestinal|strain:zebrafish|tissue:intestinal|age:5dpf|treatment:BP 5 exposure,BP 3 3,Illumina HiSeqTM 2500 used for basecalling. specific steps were followed using the methods previously described WEI L  CAO L  MIAO Y  et al. Transcriptome analysis of Spodoptera frugiperda 9 Sf9 cells infected with baculovirus  AcMNPV or AcMNPV BmK IT [J]. Biotechnol Lett  2017  398: 1129 39. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Genome build: mm9 Supplementary files format and content: tab delimited text files include MEAN TPM values for each Sample,Intestinal,Embryos of BP 3 exposure group were incubated in 2mg/L BP 3,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer’s instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:zebrafish|tissue:intestinal|age:5dpf|treatment:BP 5 exposure,GSM5229428,GSM5229428: BP 3 3; Danio rerio; RNA Seq,GSM5229428,,1,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer's instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5229428,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP313793,,loader:fastq load.py,BP_3_3.raw_1.fastq.gz,fastq,2872993950.0,19153293.0,GSM5229428 r1,0:150,A:788453365;C:654820745;G:670796608;T:758910496;N:12736,150,,,,788453365,654820745,670796608,758910496,12736,SRX10531555,SRS8654916,SRA1215917,GEO,"Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology",1,0.94579,,0.11753,,0.64808,,0.48698,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-04-07,Larval,Larval,Gut,Digestive System
63879,SRR14163084,SRX10531554,SRS8654915,SRP313793,PRJNA720320,Quantitative Analysis of Transcriptomes of Control and BP 3 exposure embryos zebrafish by RNA sequencing,GSE171619,Transcriptome Analysis,Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without xxx 3BP 3 at the transcriptome level and find the underlying mechanism how could BP 3 impede the development of enteric nervous system. Methods:  Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos were generated by paired end sequencing  in triplicate  using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis GSEA comparing WT and BP 3 exposure groups was performed by GSEA software version 4.0.03. A nominal p value < 0.05 and false discovery rate FDR q value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. RNA seq data confirmed 159 up regulated and 73 down regulated genes in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP 3 exposure zebrafish intestinal transcriptomes  with biologic replicates  generated by RNA sequencing technology. Our results showed that 159 genes were up regulated and 73 were down regulated  in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Overall design: Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos,,,,BP 3 2,GSM5229427,,source name:Intestinal|strain:zebrafish|tissue:intestinal|age:5dpf|treatment:BP 4 exposure,BP 3 2,Illumina HiSeqTM 2500 used for basecalling. specific steps were followed using the methods previously described WEI L  CAO L  MIAO Y  et al. Transcriptome analysis of Spodoptera frugiperda 9 Sf9 cells infected with baculovirus  AcMNPV or AcMNPV BmK IT [J]. Biotechnol Lett  2017  398: 1129 39. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Genome build: mm9 Supplementary files format and content: tab delimited text files include MEAN TPM values for each Sample,Intestinal,Embryos of BP 3 exposure group were incubated in 2mg/L BP 3,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer’s instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:zebrafish|tissue:intestinal|age:5dpf|treatment:BP 4 exposure,GSM5229427,GSM5229427: BP 3 2; Danio rerio; RNA Seq,GSM5229427,,1,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer's instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5229427,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP313793,,loader:fastq load.py,BP_3_2.raw_1.fastq.gz,fastq,3893023500.0,25953490.0,GSM5229427 r1,0:150,A:1044984644;C:903846940;G:923268550;T:1020912804;N:10562,150,,,,1044984644,903846940,923268550,1020912804,10562,SRX10531554,SRS8654915,SRA1215917,GEO,"Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology",1,0.95235,,0.10204,,0.64616,,0.48004,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-04-07,Larval,Larval,Gut,Digestive System
63880,SRR14163083,SRX10531553,SRS8654914,SRP313793,PRJNA720320,Quantitative Analysis of Transcriptomes of Control and BP 3 exposure embryos zebrafish by RNA sequencing,GSE171619,Transcriptome Analysis,Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without xxx 3BP 3 at the transcriptome level and find the underlying mechanism how could BP 3 impede the development of enteric nervous system. Methods:  Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos were generated by paired end sequencing  in triplicate  using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis GSEA comparing WT and BP 3 exposure groups was performed by GSEA software version 4.0.03. A nominal p value < 0.05 and false discovery rate FDR q value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. RNA seq data confirmed 159 up regulated and 73 down regulated genes in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP 3 exposure zebrafish intestinal transcriptomes  with biologic replicates  generated by RNA sequencing technology. Our results showed that 159 genes were up regulated and 73 were down regulated  in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Overall design: Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos,,,,BP 3 1,GSM5229426,,source name:Intestinal|strain:zebrafish|tissue:intestinal|age:5dpf|treatment:BP 3 exposure,BP 3 1,Illumina HiSeqTM 2500 used for basecalling. specific steps were followed using the methods previously described WEI L  CAO L  MIAO Y  et al. Transcriptome analysis of Spodoptera frugiperda 9 Sf9 cells infected with baculovirus  AcMNPV or AcMNPV BmK IT [J]. Biotechnol Lett  2017  398: 1129 39. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Genome build: mm9 Supplementary files format and content: tab delimited text files include MEAN TPM values for each Sample,Intestinal,Embryos of BP 3 exposure group were incubated in 2mg/L BP 3,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer’s instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:zebrafish|tissue:intestinal|age:5dpf|treatment:BP 3 exposure,GSM5229426,GSM5229426: BP 3 1; Danio rerio; RNA Seq,GSM5229426,,1,intestinal tissues of embryos were dissected by microforceps. All samples were stored at −80°C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer's instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5229426,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP313793,,loader:fastq load.py,BP_3_1.raw_1.fastq.gz,fastq,4744955850.0,31633039.0,GSM5229426 r1,0:150,A:1276837334;C:1108509625;G:1137266780;T:1222329367;N:12744,150,,,,1276837334,1108509625,1137266780,1222329367,12744,SRX10531553,SRS8654914,SRA1215917,GEO,"Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology",1,0.95279,,0.10142,,0.6496,,0.48144,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-04-07,Larval,Larval,Gut,Digestive System
63907,SRR14213386,SRX10579904,SRS8684372,SRP314470,PRJNA721381,RNA Seq from zebrafish adult tissues,GSE171906,Transcriptome Analysis,The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.,,pubmed:34556579,,Intestine3,GSM5237128,,source name:zebrafish intestine|genotype:wild type|tissue:intestine|strain:TLAB,Intestine3,Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM,zebrafish intestine,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:intestine|strain:TLAB,GSM5237128,GSM5237128: Intestine3; Danio rerio; RNA Seq,GSM5237128,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM5237128,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP314470,,,Intestine3.fastq,fastq,1569173300.0,15691733.0,GSM5237128 r1,0:100,A:386685730;C:390640575;G:379186629;T:412599551;N:60815,100,,,,386685730,390640575,379186629,412599551,60815,SRX10579904,SRS8684372,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95006,,0.08193,,0.78015,,0.56907,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2021-04-12,Undetermined,Undetermined,Gut,Digestive System
63908,SRR14213385,SRX10579903,SRS8684371,SRP314470,PRJNA721381,RNA Seq from zebrafish adult tissues,GSE171906,Transcriptome Analysis,The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.,,pubmed:34556579,,Intestine2,GSM5237127,,source name:zebrafish intestine|genotype:wild type|tissue:intestine|strain:TLAB,Intestine2,Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM,zebrafish intestine,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:intestine|strain:TLAB,GSM5237127,GSM5237127: Intestine2; Danio rerio; RNA Seq,GSM5237127,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM5237127,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP314470,,,Intestine2.fastq,fastq,2130566800.0,21305668.0,GSM5237127 r1,0:100,A:526261017;C:530944116;G:514882717;T:558396882;N:82068,100,,,,526261017,530944116,514882717,558396882,82068,SRX10579903,SRS8684371,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95,,0.0797,,0.77382,,0.56644,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2021-04-12,Undetermined,Undetermined,Gut,Digestive System
63909,SRR14213384,SRX10579902,SRS8684370,SRP314470,PRJNA721381,RNA Seq from zebrafish adult tissues,GSE171906,Transcriptome Analysis,The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.,,pubmed:34556579,,Intestine1,GSM5237126,,source name:zebrafish intestine|genotype:wild type|tissue:intestine|strain:TLAB,Intestine1,Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM,zebrafish intestine,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:intestine|strain:TLAB,GSM5237126,GSM5237126: Intestine1; Danio rerio; RNA Seq,GSM5237126,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM5237126,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP314470,,,Intestine1.fastq,fastq,1573976900.0,15739769.0,GSM5237126 r1,0:100,A:387753454;C:390843684;G:380063787;T:415255739;N:60236,100,,,,387753454,390843684,380063787,415255739,60236,SRX10579902,SRS8684370,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95269,,0.07992,,0.77311,,0.57635,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2021-04-12,Undetermined,Undetermined,Gut,Digestive System