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168 rows where experiment.library_layout = "SINGLE", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Digestive System"

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devstage_curation_coarse 6

devstage_curation 6

experiment.library_selection 4

technology 3

tissue_curation_coarse 1

  • Digestive System · 168 ✖

tissue_curation 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 168 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 168 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
32 32 DRR408242 DRX393848 DRS407006 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 3 zebrafish adult gut replicate 3 SAMD00529462   sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529462 DRX393848 AR019 gut 6 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529462       3546347364.0 28145614.0 DRR408242 0:126 1:0 A:919466631;C:829424335;G:818581155;T:978810217;N:65026 126 0     919466631 829424335 818581155 978810217 65026 DRX393848 DRS407006 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
33 33 DRR408241 DRX393847 DRS407005 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 2 zebrafish adult gut replicate 2 SAMD00529461   sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529461 DRX393847 AR006 gut 4 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529461       3671973648.0 29142648.0 DRR408241 0:126 1:0 A:942167543;C:859431290;G:852661772;T:1017643011;N:70032 126 0     942167543 859431290 852661772 1017643011 70032 DRX393847 DRS407005 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
34 34 DRR408240 DRX393846 DRS407004 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 1 zebrafish adult gut replicate 1 SAMD00529460   sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529460 DRX393846 AR004 gut 2 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529460       3480523704.0 27623204.0 DRR408240 0:126 1:0 A:898051986;C:827557593;G:816541244;T:938307607;N:65274 126 0     898051986 827557593 816541244 938307607 65274 DRX393846 DRS407004 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
35 35 DRR408239 DRX393845 DRS407003 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 3 zebrafish larval gut replicate 3 SAMD00529459   sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529459 DRX393845 AR012 gut 5 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529459       3463982046.0 27491921.0 DRR408239 0:126 1:0 A:842552557;C:849757648;G:837664725;T:933942026;N:65090 126 0     842552557 849757648 837664725 933942026 65090 DRX393845 DRS407003 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
36 36 DRR408238 DRX393844 DRS407002 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 2 zebrafish larval gut replicate 2 SAMD00529458   sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529458 DRX393844 AR005 gut 3 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529458       3782320416.0 30018416.0 DRR408238 0:126 1:0 A:930337206;C:920645770;G:906559955;T:1024704277;N:73208 126 0     930337206 920645770 906559955 1024704277 73208 DRX393844 DRS407002 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
37 37 DRR408237 DRX393843 DRS407001 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 1 zebrafish larval gut replicate 1 SAMD00529457   sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529457 DRX393843 AR002 gut 1 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529457       3606885828.0 28626078.0 DRR408237 0:126 1:0 A:879148446;C:885673723;G:870330963;T:971663212;N:69484 126 0     879148446 885673723 870330963 971663212 69484 DRX393843 DRS407001 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
172 172 DRR075398 DRX069312 DRS075493 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The gut of control fish 7dpf Control gut SAMD00065412   sample name:2 control gut 150701 Hiseq3A l3 018|tissue type:Gut                 Illumina HiSeq 2500 sequencing of SAMD00065412 DRX069312 Control gut 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065412       1008093492.0 28002597.0 DRR075398 0:36 A:230431417;C:251640901;G:244174255;T:281811580;N:35339 36       230431417 251640901 244174255 281811580 35339 DRX069312 DRS075493 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.9173   0.07181   0.72017   0.45193   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Gut Digestive System
9166 9166 ERR2788341 ERX2797590 ERS2709706 ERP110806 PRJEB28589 Single cell transcriptional analysis reveals ILC like cells in zebrafish E-MTAB-7159 Transcriptome Analysis Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11   Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's … 5149STDY7292228 SAMEA4890710 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female 1 male|strain:AB                 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish E MTAB 7159:5149STDY7292228 p 5149STDY7292228 p Single cell transcriptional analysis reveals ILC like cells in zebrafish The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B… Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7292228.bam 5149STDY7292228.bam.bai bam bam 37970494940.0 387454030.0 E MTAB 7159:5149STDY7292228 0:98 A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108 98       11476520187 7571635167 8189594199 10701044279 31701108 ERX2797590 ERS2709706 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.87568   0.2122   0.82582   0.5259   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
9167 9167 ERR2788340 ERX2797589 ERS2709705 ERP110806 PRJEB28589 Single cell transcriptional analysis reveals ILC like cells in zebrafish E-MTAB-7159 Transcriptome Analysis Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11   Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's … 5149STDY7274848 SAMEA4890709 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB                 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish E MTAB 7159:5149STDY7274848 p 5149STDY7274848 p Single cell transcriptional analysis reveals ILC like cells in zebrafish The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B… Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7274848.bam 5149STDY7274848.bam.bai bam bam 34517322840.0 352217580.0 E MTAB 7159:5149STDY7274848 0:98 A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273 98       10635243399 6658515314 7525079510 9695995344 2489273 ERX2797589 ERS2709705 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.86206   0.18065   0.83514   0.53609   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
9168 9168 ERR2788339 ERX2797588 ERS2709704 ERP110806 PRJEB28589 Single cell transcriptional analysis reveals ILC like cells in zebrafish E-MTAB-7159 Transcriptome Analysis Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11   Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's … 5149STDY7274847 SAMEA4890708 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB                 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish E MTAB 7159:5149STDY7274847 p 5149STDY7274847 p Single cell transcriptional analysis reveals ILC like cells in zebrafish The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B… Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7274847.bam 5149STDY7274847.bam.bai bam bam 34467649678.0 351710711.0 E MTAB 7159:5149STDY7274847 0:98 A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266 98       10609988948 6722093635 7464497879 9667814950 3254266 ERX2797588 ERS2709704 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.88751   0.21835   0.83771   0.53927   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
9169 9169 ERR2788338 ERX2797587 ERS2709703 ERP110806 PRJEB28589 Single cell transcriptional analysis reveals ILC like cells in zebrafish E-MTAB-7159 Transcriptome Analysis Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11   Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's … 5149STDY7274846 SAMEA4890707 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB                 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish E MTAB 7159:5149STDY7274846 p 5149STDY7274846 p Single cell transcriptional analysis reveals ILC like cells in zebrafish The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B… Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP110806 Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL 5149STDY7274846.bam 5149STDY7274846.bam.bai bam bam 35052538472.0 357678964.0 E MTAB 7159:5149STDY7274846 0:98 A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277 98       10698116265 6858102477 7626019661 9866905792 3394277 ERX2797587 ERS2709703 ERA1594569 Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive 1 0.88916   0.21537   0.83802   0.5336   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2018-09-11 Adult Adult Gut Digestive System
41072 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
62742 62742 SRR13360748 SRX9785053 SRS7972286 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM2 PM2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm2_S8_R1_001.fastq.gz fastq 3517898944.0 46288144.0 pm2 S8 R1 001.fastq.gz 0:76 1:0 A:914616261;C:828363626;G:805674434;T:969167482;N:77141 76 0     914616261 828363626 805674434 969167482 77141 SRX9785053 SRS7972286 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.94008   0.0747   0.71394   0.51572   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62743 62743 SRR13360749 SRX9785052 SRS7972285 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM1 PM1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm1_S7_R1_001.fastq.gz fastq 1974822380.0 25984505.0 pm1 S7 R1 001.fastq.gz 0:76 1:0 A:561606319;C:416363486;G:408486827;T:588324386;N:41362 76 0     561606319 416363486 408486827 588324386 41362 SRX9785052 SRS7972285 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.9274   0.16109   0.74351   0.57108   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62744 62744 SRR13360750 SRX9785051 SRS7972284 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP4 CP4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp4_S4_R1_001.fastq.gz fastq 2913402316.0 38334241.0 cp4 S4 R1 001.fastq.gz 0:76 1:0 A:791131658;C:648321809;G:621173454;T:852725371;N:50024 76 0     791131658 648321809 621173454 852725371 50024 SRX9785051 SRS7972284 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93191   0.1275   0.7333   0.55298   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62745 62745 SRR13360751 SRX9785050 SRS7972283 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP3 CP3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp3_S6_R1_001.fastq.gz fastq 2648220684.0 34845009.0 cp3 S6 R1 001.fastq.gz 0:76 1:0 A:697194378;C:597685138;G:585283565;T:767999519;N:58084 76 0     697194378 597685138 585283565 767999519 58084 SRX9785050 SRS7972283 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93629   0.1048   0.7349   0.54364   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62746 62746 SRR13360752 SRX9785049 SRS7972282 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP2 CP2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp2_S5_R1_001.fastq.gz fastq 2339410872.0 30781722.0 cp2 S5 R1 001.fastq.gz 0:76 1:0 A:620056592;C:539298564;G:520500416;T:659503250;N:52050 76 0     620056592 539298564 520500416 659503250 52050 SRX9785049 SRS7972282 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93909   0.0916   0.70942   0.51709   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62747 62747 SRR13360753 SRX9785048 SRS7972281 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       soybean soybean1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CP1 CP1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cp1_S4_R1_001.fastq.gz fastq 2271445592.0 29887442.0 cp1 S4 R1 001.fastq.gz 0:76 1:0 A:620595380;C:508382666;G:499686333;T:642731924;N:49289 76 0     620595380 508382666 499686333 642731924 49289 SRX9785048 SRS7972281 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93497   0.1129   0.71127   0.50787   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62748 62748 SRR13360754 SRX9785047 SRS7972280 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ4 CZ4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz4_S1_R1_001.fastq.gz fastq 2772612848.0 36481748.0 cz4 S1 R1 001.fastq.gz 0:76 1:0 A:753409223;C:625962831;G:590503241;T:802690640;N:46913 76 0     753409223 625962831 590503241 802690640 46913 SRX9785047 SRS7972280 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.92942   0.15362   0.62889   0.51867   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62749 62749 SRR13360755 SRX9785046 SRS7972279 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ3 CZ3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz3_S3_R1_001.fastq.gz fastq 2424287672.0 31898522.0 cz3 S3 R1 001.fastq.gz 0:76 1:0 A:629966430;C:571438897;G:558947157;T:663881953;N:53235 76 0     629966430 571438897 558947157 663881953 53235 SRX9785046 SRS7972279 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.94199   0.04836   0.72218   0.48478   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62750 62750 SRR13360756 SRX9785045 SRS7972278 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM4 PM4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm4_S7_R1_001.fastq.gz fastq 2901513560.0 38177810.0 pm4 S7 R1 001.fastq.gz 0:76 1:0 A:737189471;C:698799076;G:664901115;T:800575145;N:48753 76 0     737189471 698799076 664901115 800575145 48753 SRX9785045 SRS7972278 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.95173   0.04367   0.74089   0.50116   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62751 62751 SRR13360757 SRX9785044 SRS7972277 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       macrogard macrogard3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae PM3 PM3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     pm3_S9_R1_001.fastq.gz fastq 3148390744.0 41426194.0 pm3 S9 R1 001.fastq.gz 0:76 1:0 A:834545372;C:725073648;G:704241250;T:884462724;N:67750 76 0     834545372 725073648 704241250 884462724 67750 SRX9785044 SRS7972277 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.94256   0.09248   0.72099   0.52303   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62752 62752 SRR13360758 SRX9785043 SRS7972276 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ2 CZ2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz2_S2_R1_001.fastq fastq 2207708116.0 29048791.0 cz2 S2 R1 001.fastq 0:76 1:0 A:614048827;C:488071931;G:474165427;T:631372646;N:49285 76 0     614048827 488071931 474165427 631372646 49285 SRX9785043 SRS7972276 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93271   0.12538   0.71733   0.53166   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62753 62753 SRR13360759 SRX9785042 SRS7972275 SRP300470 PRJNA689790 Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish PRJNA689790 Other We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.       control control1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae CZ1 CZ1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 550   SRP300470     cz1_S1_R1_001.fastq.gz fastq 2264115696.0 29790996.0 cz1 S1 R1 001.fastq.gz 0:76 1:0 A:619936364;C:496981021;G:501038961;T:646109550;N:49800 76 0     619936364 496981021 501038961 646109550 49800 SRX9785042 SRS7972275 SRA1180489 Nord University|Faculty of Bioscience Nord University 1 0.93737   0.1307   0.73003   0.55416   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2021-01-05 Juvenile Juvenile Gut Digestive System
62981 62981 SRR13559185 SRX9957470 SRS8131854 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       100% feeding group replicate 2 CR 100perc 2   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:100% feeding|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 100% feeding CR 100perc 2 CR 100perc 2 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_100perc_2_S10_R1_001.fastq.gz fastq 1797322363.0 23790604.0 CR 100perc 2 S10 R1 001.fastq.gz 0:75.55 1:0 A:430558741;C:468161000;G:471226375;T:427297574;N:78673 75 0     430558741 468161000 471226375 427297574 78673 SRX9957470 SRS8131854 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.65722   0.19871   0.82339   0.66254   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62982 62982 SRR13559186 SRX9957469 SRS8131853 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       100% feeding group replicate 1 CR 100perc 1   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:100% feeding|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 100% feeding CR 100perc 1 CR 100perc 1 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_100perc_1_S9_R1_001.fastq.gz fastq 1534720214.0 20317497.0 CR 100perc 1 S9 R1 001.fastq.gz 0:75.54 1:0 A:375776426;C:394418295;G:367506580;T:396953400;N:65513 75 0     375776426 394418295 367506580 396953400 65513 SRX9957469 SRS8131853 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.84461   0.26652   0.76717   0.62282   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62983 62983 SRR13559187 SRX9957468 SRS8131852 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       85% feeding group replicate 4 CR 85perc 4   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:85% feeding|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 85% feeding CR 85perc 4 CR 85perc 4 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_85perc_4_S8_R1_001.fastq.gz fastq 1916818437.0 25373905.0 CR 85perc 4 S8 R1 001.fastq.gz 0:75.54 1:0 A:488054788;C:475184415;G:443451608;T:510046224;N:81402 75 0     488054788 475184415 443451608 510046224 81402 SRX9957468 SRS8131852 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.92737   0.2783   0.75909   0.57435   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62984 62984 SRR13559188 SRX9957467 SRS8131851 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       85% feeding group replicate 3 CR 85perc 3   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:85% feeding|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 85% feeding CR 85perc 3 CR 85perc 3 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_85perc_3_S7_R1_001.fastq.gz fastq 1843871333.0 24411281.0 CR 85perc 3 S7 R1 001.fastq.gz 0:75.53 1:0 A:441643488;C:487987766;G:446957305;T:467206076;N:76698 75 0     441643488 487987766 446957305 467206076 76698 SRX9957467 SRS8131851 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.91984   0.25275   0.77565   0.65163   74   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62985 62985 SRR13559189 SRX9957466 SRS8131850 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       85% feeding group replicate 2 CR 85perc 2   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:85% feeding|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 85% feeding CR 85perc 2 CR 85perc 2 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_85perc_2_S6_R1_001.fastq.gz fastq 2063663358.0 27321356.0 CR 85perc 2 S6 R1 001.fastq.gz 0:75.53 1:0 A:495156958;C:545615457;G:490454848;T:532349272;N:86823 75 0     495156958 545615457 490454848 532349272 86823 SRX9957466 SRS8131850 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.92542   0.29093   0.77743   0.62803   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System

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