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
25135,SRR25649156,SRX21375305,SRS18618397,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X8,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X8,18689X8,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X8_R1.fastq.gz 18689X8_R2.fastq.gz,fastq fastq,8163984120.0,27033060.0,18689X8 R1.fastq.gz,0:151 1:151,A:1900143724;C:2183735704;G:2147710753;T:1932229591;N:164348,151,151,,,1900143724,2183735704,2147710753,1932229591,164348,SRX21375305,SRS18618397,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89288,0.89479,0.20193,0.20116,0.79072,0.79352,0.57246,0.56409,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25136,SRR25649157,SRX21375304,SRS18618396,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X15,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X15,19629X15,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X15_R2.fastq.gz 19629X15_R1.fastq.gz,fastq fastq,10277997106.0,34033103.0,19629X15 R1.fastq.gz,0:151 1:151,A:2798108841;C:2341310321;G:2438634645;T:2699729301;N:213998,151,151,,,2798108841,2341310321,2438634645,2699729301,213998,SRX21375304,SRS18618396,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90655,0.90714,0.18082,0.18027,0.72803,0.72953,0.45722,0.45335,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25137,SRR25649158,SRX21375303,SRS18618395,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X14,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 3|replicate:T2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X14,19629X14,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X14_R1.fastq.gz 19629X14_R2.fastq.gz,fastq fastq,10921707086.0,36164593.0,19629X14 R1.fastq.gz,0:151 1:151,A:2969229092;C:2484790148;G:2595052715;T:2872407360;N:227771,151,151,,,2969229092,2484790148,2595052715,2872407360,227771,SRX21375303,SRS18618395,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90015,0.90211,0.19548,0.19546,0.72997,0.73131,0.53978,0.54998,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25138,SRR25649159,SRX21375302,SRS18618394,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X13,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X13,19629X13,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X13_R1.fastq.gz 19629X13_R2.fastq.gz,fastq fastq,10019262230.0,33176365.0,19629X13 R1.fastq.gz,0:151 1:151,A:2732766602;C:2270429150;G:2391166434;T:2624690350;N:209694,151,151,,,2732766602,2270429150,2391166434,2624690350,209694,SRX21375302,SRS18618394,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90381,0.90536,0.18425,0.18388,0.72681,0.72936,0.48627,0.49398,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25139,SRR25649160,SRX21375301,SRS18618393,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X12,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X12,19629X12,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X12_R1.fastq.gz 19629X12_R2.fastq.gz,fastq fastq,11078632326.0,36684213.0,19629X12 R1.fastq.gz,0:151 1:151,A:2995473302;C:2550446088;G:2653594689;T:2878887522;N:230725,151,151,,,2995473302,2550446088,2653594689,2878887522,230725,SRX21375301,SRS18618393,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91101,0.91121,0.16145,0.16142,0.70274,0.70498,0.47852,0.48788,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25140,SRR25649161,SRX21375300,SRS18618392,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X11,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X11,19629X11,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X11_R1.fastq.gz 19629X11_R2.fastq.gz,fastq fastq,10957183630.0,36282065.0,19629X11 R1.fastq.gz,0:151 1:151,A:2987773085;C:2485587980;G:2603747193;T:2879845340;N:230032,151,151,,,2987773085,2485587980,2603747193,2879845340,230032,SRX21375300,SRS18618392,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91198,0.91301,0.20992,0.20926,0.73044,0.73316,0.44301,0.43596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25141,SRR25649162,SRX21375299,SRS18618390,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X10,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X10,19629X10,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X10_R1.fastq.gz 19629X10_R2.fastq.gz,fastq fastq,9549065142.0,31619421.0,19629X10 R1.fastq.gz,0:151 1:151,A:2603092155;C:2167963952;G:2264536965;T:2513273275;N:198795,151,151,,,2603092155,2167963952,2264536965,2513273275,198795,SRX21375299,SRS18618390,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.92549,0.92615,0.16176,0.15925,0.7683,0.76926,0.3093,0.30927,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25144,SRR25649165,SRX21375296,SRS18618388,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X6,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X6,18843X6,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X6_R1.fastq.gz 18843X6_R2.fastq.gz,fastq fastq,8690806510.0,28777505.0,18843X6 R1.fastq.gz,0:151 1:151,A:2346658651;C:2002583855;G:2108507319;T:2232918222;N:138463,151,151,,,2346658651,2002583855,2108507319,2232918222,138463,SRX21375296,SRS18618388,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91741,0.91785,0.21796,0.21778,0.6971,0.70102,0.49123,0.51016,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25147,SRR25649168,SRX21375293,SRS18618385,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X3,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X3,18843X3,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X3_R1.fastq.gz 18843X3_R2.fastq.gz,fastq fastq,9351018676.0,30963638.0,18843X3 R1.fastq.gz,0:151 1:151,A:2555870224;C:2133006230;G:2246501165;T:2415491618;N:149439,151,151,,,2555870224,2133006230,2246501165,2415491618,149439,SRX21375293,SRS18618385,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91594,0.91512,0.21678,0.21621,0.72719,0.73117,0.52961,0.53327,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25149,SRR25649170,SRX21375291,SRS18618383,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X9,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X9,19629X9,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X9_R1.fastq.gz 19629X9_R2.fastq.gz,fastq fastq,12342730940.0,40869970.0,19629X9 R1.fastq.gz,0:151 1:151,A:3339874828;C:2828928610;G:2945452577;T:3228218292;N:256633,151,151,,,3339874828,2828928610,2945452577,3228218292,256633,SRX21375291,SRS18618383,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90738,0.8127,0.19825,0.17409,0.73385,0.74659,0.54306,0.55304,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25151,SRR25649172,SRX21375289,SRS18618381,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X5,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X5,18689X5,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X5_R1.fastq.gz 18689X5_R2.fastq.gz,fastq fastq,8136028886.0,26940493.0,18689X5 R1.fastq.gz,0:151 1:151,A:2015403368;C:2051480513;G:2023331135;T:2045661742;N:152128,151,151,,,2015403368,2051480513,2023331135,2045661742,152128,SRX21375289,SRS18618381,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88067,0.88216,0.24575,0.2425,0.75018,0.75073,0.59361,0.61451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25154,SRR25649175,SRX21375286,SRS18618378,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X9,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X9,18843X9,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X9_R1.fastq.gz 18843X9_R2.fastq.gz,fastq fastq,8819654206.0,29204153.0,18843X9 R1.fastq.gz,0:151 1:151,A:2383706177;C:2044504407;G:2140881818;T:2250422256;N:139548,151,151,,,2383706177,2044504407,2140881818,2250422256,139548,SRX21375286,SRS18618378,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90385,0.90437,0.21274,0.21235,0.72604,0.73164,0.52888,0.52909,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25157,SRR25649178,SRX21375283,SRS18618375,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X7,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X7,18689X7,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X7_R1.fastq.gz 18689X7_R2.fastq.gz,fastq fastq,8986035368.0,29755084.0,18689X7 R1.fastq.gz,0:151 1:151,A:2169723143;C:2326462981;G:2292317481;T:2197350043;N:181720,151,151,,,2169723143,2326462981,2292317481,2197350043,181720,SRX21375283,SRS18618375,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89254,0.89285,0.22562,0.22356,0.74911,0.75089,0.6409,0.65585,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25160,SRR25649181,SRX21375280,SRS18618372,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X8,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X8,19629X8,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X8_R2.fastq.gz 19629X8_R1.fastq.gz,fastq fastq,10758135430.0,35622965.0,19629X8 R1.fastq.gz,0:151 1:151,A:2991372806;C:2398155523;G:2517276916;T:2851104238;N:225947,151,151,,,2991372806,2398155523,2517276916,2851104238,225947,SRX21375280,SRS18618372,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88839,0.89055,0.23357,0.23344,0.72592,0.72851,0.53343,0.53081,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25161,SRR25649182,SRX21375279,SRS18618371,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X7,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X7,19629X7,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X7_R1.fastq.gz 19629X7_R2.fastq.gz,fastq fastq,11738178884.0,38868142.0,19629X7 R1.fastq.gz,0:151 1:151,A:3192358555;C:2674045852;G:2784070515;T:3087458659;N:245303,151,151,,,3192358555,2674045852,2784070515,3087458659,245303,SRX21375279,SRS18618371,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.9074,0.90829,0.20853,0.20916,0.74115,0.74369,0.53704,0.55385,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
56883,SRR11178131,SRX7798810,SRS6213687,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry negative 5,GSM4338415,,source name:Adult gut sox10:cre;Cherry negative|tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry negative 5,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry negative,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,GSM4338415,GSM4338415: Adult gut sox10:cre;Cherry negative 5; Danio rerio; RNA Seq,GSM4338415,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338415,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_neg_5_R1.fastq.gz PE_neg_5_R2.fastq.gz,fastq fastq,7402006796.0,36643598.0,GSM4338415 r1,0:101 1:101,A:2141100609;C:1495392069;G:1539459100;T:2225819644;N:235374,101,101,,,2141100609,1495392069,1539459100,2225819644,235374,SRX7798810,SRS6213687,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.79957,0.80443,0.53128,0.53529,0.74728,0.75968,0.53126,0.55373,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56884,SRR11178130,SRX7798809,SRS6213686,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry negative 4,GSM4338414,,source name:Adult gut sox10:cre;Cherry negative|tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry negative 4,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry negative,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,GSM4338414,GSM4338414: Adult gut sox10:cre;Cherry negative 4; Danio rerio; RNA Seq,GSM4338414,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338414,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_neg_4_R1.fastq.gz PE_neg_4_R2.fastq.gz,fastq fastq,6742235406.0,33377403.0,GSM4338414 r1,0:101 1:101,A:1943591079;C:1353703348;G:1421710867;T:2023006494;N:223618,101,101,,,1943591079,1353703348,1421710867,2023006494,223618,SRX7798809,SRS6213686,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.77924,0.7849,0.57144,0.57418,0.74612,0.76177,0.55304,0.49173,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56885,SRR11178129,SRX7798808,SRS6213685,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry negative 3,GSM4338413,,source name:Adult gut sox10:cre;Cherry negative|tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry negative 3,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry negative,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,GSM4338413,GSM4338413: Adult gut sox10:cre;Cherry negative 3; Danio rerio; RNA Seq,GSM4338413,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338413,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_neg_3_R2.fastq.gz PE_neg_3_R1.fastq.gz,fastq fastq,6277972140.0,31079070.0,GSM4338413 r1,0:101 1:101,A:1793266465;C:1274475049;G:1339662110;T:1870363568;N:204948,101,101,,,1793266465,1274475049,1339662110,1870363568,204948,SRX7798808,SRS6213685,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.77642,0.78334,0.54202,0.54381,0.75564,0.76467,0.55282,0.55504,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56886,SRR11178128,SRX7798807,SRS6213684,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry negative 2,GSM4338412,,source name:Adult gut sox10:cre;Cherry negative|tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry negative 2,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry negative,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,GSM4338412,GSM4338412: Adult gut sox10:cre;Cherry negative 2; Danio rerio; RNA Seq,GSM4338412,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338412,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_neg_2_R1.fastq.gz PE_neg_2_R2.fastq.gz,fastq fastq,6124177824.0,30317712.0,GSM4338412 r1,0:101 1:101,A:1748043042;C:1241789616;G:1297992638;T:1836153062;N:199466,101,101,,,1748043042,1241789616,1297992638,1836153062,199466,SRX7798807,SRS6213684,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.80191,0.80757,0.51449,0.51588,0.76504,0.77477,0.54934,0.55455,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56887,SRR11178127,SRX7798806,SRS6213683,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry negative 1,GSM4338411,,source name:Adult gut sox10:cre;Cherry negative|tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry negative 1,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry negative,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA,GSM4338411,GSM4338411: Adult gut sox10:cre;Cherry negative 1; Danio rerio; RNA Seq,GSM4338411,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338411,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_neg_1_R1.fastq.gz PE_neg_1_R2.fastq.gz,fastq fastq,6589632890.0,32621945.0,GSM4338411 r1,0:101 1:101,A:1823414720;C:1397729205;G:1451531094;T:1916757475;N:200396,101,101,,,1823414720,1397729205,1451531094,1916757475,200396,SRX7798806,SRS6213683,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.76935,0.77393,0.42629,0.4289,0.75215,0.7623,0.60804,0.60753,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56888,SRR11178126,SRX7798805,SRS6213682,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry positive 5,GSM4338410,,source name:Adult gut sox10:cre;Cherry positive|tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry positive 5,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry positive,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,GSM4338410,GSM4338410: Adult gut sox10:cre;Cherry positive 5; Danio rerio; RNA Seq,GSM4338410,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338410,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_SOX10_5_R2.fastq.gz PE_SOX10_5_R1.fastq.gz,fastq fastq,6227107530.0,30827265.0,GSM4338410 r1,0:101 1:101,A:1778260787;C:1263522409;G:1325803201;T:1859318656;N:202477,101,101,,,1778260787,1263522409,1325803201,1859318656,202477,SRX7798805,SRS6213682,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.75911,0.76709,0.54861,0.55238,0.76055,0.77112,0.50252,0.50202,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56889,SRR11178125,SRX7798804,SRS6213681,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry positive 4,GSM4338409,,source name:Adult gut sox10:cre;Cherry positive|tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry positive 4,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry positive,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,GSM4338409,GSM4338409: Adult gut sox10:cre;Cherry positive 4; Danio rerio; RNA Seq,GSM4338409,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338409,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_SOX10_4_R1.fastq.gz PE_SOX10_4_R2.fastq.gz,fastq fastq,6663194422.0,32986111.0,GSM4338409 r1,0:101 1:101,A:1895061091;C:1371909397;G:1428534811;T:1967470043;N:219080,101,101,,,1895061091,1371909397,1428534811,1967470043,219080,SRX7798804,SRS6213681,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.76901,0.7763,0.52292,0.52528,0.75134,0.76301,0.54114,0.5458,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56890,SRR11178124,SRX7798803,SRS6213680,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry positive 3,GSM4338408,,source name:Adult gut sox10:cre;Cherry positive|tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry positive 3,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry positive,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,GSM4338408,GSM4338408: Adult gut sox10:cre;Cherry positive 3; Danio rerio; RNA Seq,GSM4338408,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338408,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_SOX10_3_R1.fastq.gz PE_SOX10_3_R2.fastq.gz,fastq fastq,7499507954.0,37126277.0,GSM4338408 r1,0:101 1:101,A:2127228605;C:1562887642;G:1607322285;T:2201830182;N:239240,101,101,,,2127228605,1562887642,1607322285,2201830182,239240,SRX7798803,SRS6213680,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.80856,0.81106,0.52726,0.52783,0.76544,0.77366,0.52717,0.5275,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56891,SRR11178123,SRX7798802,SRS6213679,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry positive 2,GSM4338407,,source name:Adult gut sox10:cre;Cherry positive|tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry positive 2,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry positive,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,GSM4338407,GSM4338407: Adult gut sox10:cre;Cherry positive 2; Danio rerio; RNA Seq,GSM4338407,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338407,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_SOX10_2_R1.fastq.gz PE_SOX10_2_R2.fastq.gz,fastq fastq,7099587546.0,35146473.0,GSM4338407 r1,0:101 1:101,A:2021294861;C:1462944139;G:1518628659;T:2096489700;N:230187,101,101,,,2021294861,1462944139,1518628659,2096489700,230187,SRX7798802,SRS6213679,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.77741,0.7843,0.53966,0.5424,0.77431,0.78437,0.53003,0.53179,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
56892,SRR11178122,SRX7798801,SRS6213678,SRP250666,PRJNA608660,Expression analysis of adult zebrafish enteric nervous system,GSE145885,Transcriptome Analysis,The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.,,pubmed:32851974,,Adult gut sox10:cre;Cherry positive 1,GSM4338406,,source name:Adult gut sox10:cre;Cherry positive|tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,Adult gut sox10:cre;Cherry positive 1,The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.,Adult gut sox10:cre;Cherry positive,Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,N/A,tissue:adult gut|cell type:ENS|rna fraction:Nuclear mRNA,GSM4338406,GSM4338406: Adult gut sox10:cre;Cherry positive 1; Danio rerio; RNA Seq,GSM4338406,,1,Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.,GEO Accession:GSM4338406,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP250666,,,PE_SOX10_1_R1.fastq.gz PE_SOX10_1_R2.fastq.gz,fastq fastq,6873769120.0,34028560.0,GSM4338406 r1,0:101 1:101,A:1971124053;C:1404397149;G:1460488716;T:2037529839;N:229363,101,101,,,1971124053,1404397149,1460488716,2037529839,229363,SRX7798801,SRS6213678,SRA1047946,GEO,"Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute",2,0.77534,0.77956,0.54706,0.54869,0.74716,0.7582,0.51729,0.52165,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,unknown,bulk,bulk,bulk,,United Kingdom,2020-02-25,Adult,Adult,Gut,Digestive System
61611,SRR12877274,SRX9343286,SRS7566335,SRP288161,PRJNA670669,Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish,GSE159845,Transcriptome Analysis,We conducted a whole genome transcriptome analysis to examine significant gene expression changes in the gut tissue of macrophage deficient irf8 mutants compared with their heterozygous sibling guts. Overall design: RNAseq dataset of mRNA libraries made from whole gut total RNA isolated from adult zebrafish: two irf8 heterozyous animals and two irf8 homozygous mutants.,,pubmed:30304682,,whole gut total RNA  st95 mut2,GSM4848259,,source name:whole gut total RNA  st95 mut|age:adult|genotype/variation:irf8 homozygous mutant|tissue:intestine,whole gut total RNA  st95 mut2,Alignment of reads to the UCSC GRCz10/danRer10 genome build using BBmap v37.99 assigning ambiguous reads randomly Calculating gene counts using the featureCounts tool in the Subread suite v1.5.2 with UCSC annotations Analysis of differential gene expressions with DESeq2 R v3.3.1 Genome build: GRCz10/danRer10 Supplementary files format and content: gene counts using featureCounts tool; genes short list from analysis using CLC Genomics Workbench 9 ,whole gut total RNA  st95 mut,no treatment,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,for details see Earley et al.  2018 Cell Reports,age:adult|genotype/variation:irf8 homozygous mutant|tissue:intestine,GSM4848259,GSM4848259: whole gut total RNA  st95 mut2; Danio rerio; RNA Seq,GSM4848259,,1,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,GEO Accession:GSM4848259,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP288161,,,ZEB_004-gut-mut2_Organ_TGACCA_L007_R1_001.fastq.gz ZEB_004-gut-mut2_Organ_TGACCA_L007_R2_001.fastq.gz,fastq fastq,4062823000.0,16251292.0,GSM4848259 r1,0:125 1:125,A:1108766687;C:919469773;G:949638400;T:1084429540;N:518600,125,125,,,1108766687,919469773,949638400,1084429540,518600,SRX9343286,SRS7566335,SRA1146317,GEO,UNC Chapel Hill,2,0.95191,0.95542,0.07163,0.07272,0.78206,0.77514,0.62305,0.61216,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,bulk,bulk,bulk,,United States,2020-10-22,Adult,Adult,Gut,Digestive System
61612,SRR12877273,SRX9343285,SRS7566337,SRP288161,PRJNA670669,Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish,GSE159845,Transcriptome Analysis,We conducted a whole genome transcriptome analysis to examine significant gene expression changes in the gut tissue of macrophage deficient irf8 mutants compared with their heterozygous sibling guts. Overall design: RNAseq dataset of mRNA libraries made from whole gut total RNA isolated from adult zebrafish: two irf8 heterozyous animals and two irf8 homozygous mutants.,,pubmed:30304682,,whole gut total RNA  st95 mut1,GSM4848258,,source name:whole gut total RNA  st95 mut|age:adult|genotype/variation:irf8 homozygous mutant|tissue:intestine,whole gut total RNA  st95 mut1,Alignment of reads to the UCSC GRCz10/danRer10 genome build using BBmap v37.99 assigning ambiguous reads randomly Calculating gene counts using the featureCounts tool in the Subread suite v1.5.2 with UCSC annotations Analysis of differential gene expressions with DESeq2 R v3.3.1 Genome build: GRCz10/danRer10 Supplementary files format and content: gene counts using featureCounts tool; genes short list from analysis using CLC Genomics Workbench 9 ,whole gut total RNA  st95 mut,no treatment,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,for details see Earley et al.  2018 Cell Reports,age:adult|genotype/variation:irf8 homozygous mutant|tissue:intestine,GSM4848258,GSM4848258: whole gut total RNA  st95 mut1; Danio rerio; RNA Seq,GSM4848258,,1,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,GEO Accession:GSM4848258,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP288161,,,ZEB_003-gut-mut1_Organ_TTAGGC_L007_R1_001.fastq.gz ZEB_003-gut-mut1_Organ_TTAGGC_L007_R2_001.fastq.gz,fastq fastq,3161333750.0,12645335.0,GSM4848258 r1,0:125 1:125,A:866363507;C:708829199;G:732878242;T:852858127;N:404675,125,125,,,866363507,708829199,732878242,852858127,404675,SRX9343285,SRS7566337,SRA1146317,GEO,UNC Chapel Hill,2,0.94869,0.95379,0.07608,0.07624,0.79551,0.78871,0.6497,0.63595,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,bulk,bulk,bulk,,United States,2020-10-22,Adult,Adult,Gut,Digestive System
61613,SRR12877272,SRX9343284,SRS7566334,SRP288161,PRJNA670669,Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish,GSE159845,Transcriptome Analysis,We conducted a whole genome transcriptome analysis to examine significant gene expression changes in the gut tissue of macrophage deficient irf8 mutants compared with their heterozygous sibling guts. Overall design: RNAseq dataset of mRNA libraries made from whole gut total RNA isolated from adult zebrafish: two irf8 heterozyous animals and two irf8 homozygous mutants.,,pubmed:30304682,,whole gut total RNA  st95 het2,GSM4848257,,source name:whole gut total RNA  st95 het|age:adult|genotype/variation:irf8 heterozyous mutant|tissue:intestine,whole gut total RNA  st95 het2,Alignment of reads to the UCSC GRCz10/danRer10 genome build using BBmap v37.99 assigning ambiguous reads randomly Calculating gene counts using the featureCounts tool in the Subread suite v1.5.2 with UCSC annotations Analysis of differential gene expressions with DESeq2 R v3.3.1 Genome build: GRCz10/danRer10 Supplementary files format and content: gene counts using featureCounts tool; genes short list from analysis using CLC Genomics Workbench 9 ,whole gut total RNA  st95 het,no treatment,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,for details see Earley et al.  2018 Cell Reports,age:adult|genotype/variation:irf8 heterozyous mutant|tissue:intestine,GSM4848257,GSM4848257: whole gut total RNA  st95 het2; Danio rerio; RNA Seq,GSM4848257,,1,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,GEO Accession:GSM4848257,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP288161,,,ZEB_002-gut-het2_Organ_CGATGT_L007_R1_001.fastq.gz ZEB_002-gut-het2_Organ_CGATGT_L007_R2_001.fastq.gz,fastq fastq,4189602500.0,16758410.0,GSM4848257 r1,0:125 1:125,A:1095380151;C:989655410;G:1025433940;T:1078570720;N:562279,125,125,,,1095380151,989655410,1025433940,1078570720,562279,SRX9343284,SRS7566334,SRA1146317,GEO,UNC Chapel Hill,2,0.96351,0.96693,0.05888,0.05915,0.78362,0.78039,0.54171,0.59437,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,bulk,bulk,bulk,,United States,2020-10-22,Adult,Adult,Gut,Digestive System
61614,SRR12877271,SRX9343283,SRS7566333,SRP288161,PRJNA670669,Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish,GSE159845,Transcriptome Analysis,We conducted a whole genome transcriptome analysis to examine significant gene expression changes in the gut tissue of macrophage deficient irf8 mutants compared with their heterozygous sibling guts. Overall design: RNAseq dataset of mRNA libraries made from whole gut total RNA isolated from adult zebrafish: two irf8 heterozyous animals and two irf8 homozygous mutants.,,pubmed:30304682,,whole gut total RNA  st95 het1,GSM4848256,,source name:whole gut total RNA  st95 het|age:adult|genotype/variation:irf8 heterozyous mutant|tissue:intestine,whole gut total RNA  st95 het1,Alignment of reads to the UCSC GRCz10/danRer10 genome build using BBmap v37.99 assigning ambiguous reads randomly Calculating gene counts using the featureCounts tool in the Subread suite v1.5.2 with UCSC annotations Analysis of differential gene expressions with DESeq2 R v3.3.1 Genome build: GRCz10/danRer10 Supplementary files format and content: gene counts using featureCounts tool; genes short list from analysis using CLC Genomics Workbench 9 ,whole gut total RNA  st95 het,no treatment,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,for details see Earley et al.  2018 Cell Reports,age:adult|genotype/variation:irf8 heterozyous mutant|tissue:intestine,GSM4848256,GSM4848256: whole gut total RNA  st95 het1; Danio rerio; RNA Seq,GSM4848256,,1,Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity  low bias PCR.,GEO Accession:GSM4848256,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP288161,,,ZEB_001-gut-het1_Organ_ATCACG_L007_R1_001.fastq.gz ZEB_001-gut-het1_Organ_ATCACG_L007_R2_001.fastq.gz,fastq fastq,3171124250.0,12684497.0,GSM4848256 r1,0:125 1:125,A:871503295;C:713954532;G:737678886;T:847572328;N:415209,125,125,,,871503295,713954532,737678886,847572328,415209,SRX9343283,SRS7566333,SRA1146317,GEO,UNC Chapel Hill,2,0.95856,0.95985,0.06423,0.06395,0.82317,0.81493,0.59621,0.67219,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,bulk,bulk,bulk,,United States,2020-10-22,Adult,Adult,Gut,Digestive System
66016,SRR15831138,SRX12122776,SRS10102635,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 4,GSM5571389,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571389,GSM5571389: hnf4ahnf4gCR 4; Danio rerio; RNA Seq,GSM5571389,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571389,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_12_dMut_S12_L001_R1_001.fastq.gz 110_12_dMut_S12_L001_R2_001.fastq.gz,fastq fastq,4069359462.0,39895681.0,GSM5571389 r1,0:51 1:51,A:1040916889;C:983635204;G:972694687;T:1067328090;N:4784592,51,51,,,1040916889,983635204,972694687,1067328090,4784592,SRX12122776,SRS10102635,SRA1290854,GEO,Duke University School of Medicine,2,0.95534,0.96378,0.09424,0.09211,0.71056,0.70981,0.54327,0.54703,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66017,SRR15831139,SRX12122776,SRS10102635,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 4,GSM5571389,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571389,GSM5571389: hnf4ahnf4gCR 4; Danio rerio; RNA Seq,GSM5571389,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571389,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_12_dMut_S12_L002_R1_001.fastq.gz 110_12_dMut_S12_L002_R2_001.fastq.gz,fastq fastq,4169735622.0,40879761.0,GSM5571389 r2,0:51 1:51,A:1065908533;C:1009500384;G:996551481;T:1095107731;N:2667493,51,51,,,1065908533,1009500384,996551481,1095107731,2667493,SRX12122776,SRS10102635,SRA1290854,GEO,Duke University School of Medicine,2,0.96474,0.96552,0.09376,0.09158,0.71019,0.7095,0.53346,0.52913,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66018,SRR15831136,SRX12122775,SRS10102634,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 3,GSM5571388,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571388,GSM5571388: hnf4ahnf4gCR 3; Danio rerio; RNA Seq,GSM5571388,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571388,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_11_dMut_S11_L001_R1_001.fastq.gz 110_11_dMut_S11_L001_R2_001.fastq.gz,fastq fastq,3971384178.0,38935139.0,GSM5571388 r1,0:51 1:51,A:1004625861;C:971190042;G:958783494;T:1032105603;N:4679178,51,51,,,1004625861,971190042,958783494,1032105603,4679178,SRX12122775,SRS10102634,SRA1290854,GEO,Duke University School of Medicine,2,0.95959,0.96719,0.07017,0.06876,0.70698,0.70686,0.52258,0.52722,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66019,SRR15831137,SRX12122775,SRS10102634,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 3,GSM5571388,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571388,GSM5571388: hnf4ahnf4gCR 3; Danio rerio; RNA Seq,GSM5571388,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571388,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_11_dMut_S11_L002_R1_001.fastq.gz 110_11_dMut_S11_L002_R2_001.fastq.gz,fastq fastq,4045239114.0,39659207.0,GSM5571388 r2,0:51 1:51,A:1022818069;C:990640204;G:976408030;T:1052761654;N:2611157,51,51,,,1022818069,990640204,976408030,1052761654,2611157,SRX12122775,SRS10102634,SRA1290854,GEO,Duke University School of Medicine,2,0.96575,0.96637,0.06987,0.06849,0.70772,0.70713,0.52978,0.51859,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66020,SRR15831134,SRX12122774,SRS10102633,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 2,GSM5571387,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571387,GSM5571387: hnf4ahnf4gCR 2; Danio rerio; RNA Seq,GSM5571387,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571387,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_10_dMut_S10_L001_R1_001.fastq.gz 110_10_dMut_S10_L001_R2_001.fastq.gz,fastq fastq,4791061584.0,46971192.0,GSM5571387 r1,0:51 1:51,A:1200312820;C:1176812434;G:1171119058;T:1237177149;N:5640123,51,51,,,1200312820,1176812434,1171119058,1237177149,5640123,SRX12122774,SRS10102633,SRA1290854,GEO,Duke University School of Medicine,2,0.95941,0.96723,0.07087,0.06966,0.71214,0.7111,0.52447,0.524,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66021,SRR15831135,SRX12122774,SRS10102633,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 2,GSM5571387,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571387,GSM5571387: hnf4ahnf4gCR 2; Danio rerio; RNA Seq,GSM5571387,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571387,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_10_dMut_S10_L002_R1_001.fastq.gz 110_10_dMut_S10_L002_R2_001.fastq.gz,fastq fastq,4925299704.0,48287252.0,GSM5571387 r2,0:51 1:51,A:1233355224;C:1211521417;G:1203634095;T:1273627808;N:3161160,51,51,,,1233355224,1211521417,1203634095,1273627808,3161160,SRX12122774,SRS10102633,SRA1290854,GEO,Duke University School of Medicine,2,0.96723,0.96735,0.07204,0.0703,0.7105,0.7105,0.51778,0.52341,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66022,SRR15831132,SRX12122773,SRS10102632,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 1,GSM5571386,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571386,GSM5571386: hnf4ahnf4gCR 1; Danio rerio; RNA Seq,GSM5571386,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571386,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_9_dMut_S9_L001_R1_001.fastq.gz 110_9_dMut_S9_L001_R2_001.fastq.gz,fastq fastq,4311139854.0,42266077.0,GSM5571386 r1,0:51 1:51,A:1094232211;C:1050945374;G:1039705692;T:1121181252;N:5075325,51,51,,,1094232211,1050945374,1039705692,1121181252,5075325,SRX12122773,SRS10102632,SRA1290854,GEO,Duke University School of Medicine,2,0.95648,0.96392,0.07444,0.07282,0.70648,0.70589,0.52955,0.52926,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66023,SRR15831133,SRX12122773,SRS10102632,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4ahnf4gCR 1,GSM5571386,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4ahnf4gCR 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4a / ;hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571386,GSM5571386: hnf4ahnf4gCR 1; Danio rerio; RNA Seq,GSM5571386,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571386,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_9_dMut_S9_L002_R1_001.fastq.gz 110_9_dMut_S9_L002_R2_001.fastq.gz,fastq fastq,4419689478.0,43330289.0,GSM5571386 r2,0:51 1:51,A:1121357906;C:1079032112;G:1065474386;T:1151001367;N:2823707,51,51,,,1121357906,1079032112,1065474386,1151001367,2823707,SRX12122773,SRS10102632,SRA1290854,GEO,Duke University School of Medicine,2,0.9641,0.96569,0.07436,0.07295,0.70496,0.70487,0.51709,0.53071,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66024,SRR15831130,SRX12122772,SRS10102631,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 4,GSM5571385,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571385,GSM5571385: hnf4gCR 4; Danio rerio; RNA Seq,GSM5571385,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571385,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_8_hnf4gMut_S8_L001_R1_001.fastq.gz 110_8_hnf4gMut_S8_L001_R2_001.fastq.gz,fastq fastq,3877756950.0,38017225.0,GSM5571385 r1,0:51 1:51,A:970181055;C:959292577;G:946294070;T:997426349;N:4562899,51,51,,,970181055,959292577,946294070,997426349,4562899,SRX12122772,SRS10102631,SRA1290854,GEO,Duke University School of Medicine,2,0.96119,0.9688,0.06114,0.06002,0.7333,0.73275,0.54303,0.54388,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66025,SRR15831131,SRX12122772,SRS10102631,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 4,GSM5571385,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571385,GSM5571385: hnf4gCR 4; Danio rerio; RNA Seq,GSM5571385,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571385,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_8_hnf4gMut_S8_L002_R1_001.fastq.gz 110_8_hnf4gMut_S8_L002_R2_001.fastq.gz,fastq fastq,3968506146.0,38906923.0,GSM5571385 r2,0:51 1:51,A:992559057;C:983076140;G:968065632;T:1022268352;N:2536965,51,51,,,992559057,983076140,968065632,1022268352,2536965,SRX12122772,SRS10102631,SRA1290854,GEO,Duke University School of Medicine,2,0.96822,0.97012,0.06148,0.06036,0.72989,0.73042,0.54826,0.54948,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66026,SRR15831128,SRX12122771,SRS10102630,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 3,GSM5571384,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571384,GSM5571384: hnf4gCR 3; Danio rerio; RNA Seq,GSM5571384,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571384,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_7_hnf4gMut_S7_L001_R1_001.fastq.gz 110_7_hnf4gMut_S7_L001_R2_001.fastq.gz,fastq fastq,4540447482.0,44514191.0,GSM5571384 r1,0:51 1:51,A:1138901681;C:1116194554;G:1104655697;T:1175370666;N:5324884,51,51,,,1138901681,1116194554,1104655697,1175370666,5324884,SRX12122771,SRS10102630,SRA1290854,GEO,Duke University School of Medicine,2,0.96064,0.96917,0.05655,0.05478,0.72784,0.72693,0.53952,0.53608,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66027,SRR15831129,SRX12122771,SRS10102630,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 3,GSM5571384,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571384,GSM5571384: hnf4gCR 3; Danio rerio; RNA Seq,GSM5571384,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571384,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_7_hnf4gMut_S7_L002_R1_001.fastq.gz 110_7_hnf4gMut_S7_L002_R2_001.fastq.gz,fastq fastq,4646182314.0,45550807.0,GSM5571384 r2,0:51 1:51,A:1164783351;C:1143838879;G:1130065259;T:1204522906;N:2971919,51,51,,,1164783351,1143838879,1130065259,1204522906,2971919,SRX12122771,SRS10102630,SRA1290854,GEO,Duke University School of Medicine,2,0.968,0.96929,0.05796,0.05581,0.72667,0.72634,0.54257,0.53437,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66028,SRR15831126,SRX12122770,SRS10102628,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 2,GSM5571383,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571383,GSM5571383: hnf4gCR 2; Danio rerio; RNA Seq,GSM5571383,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571383,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_6_hnf4gMut_S6_L001_R1_001.fastq.gz 110_6_hnf4gMut_S6_L001_R2_001.fastq.gz,fastq fastq,3757499664.0,36838232.0,GSM5571383 r1,0:51 1:51,A:945319095;C:920831833;G:912749408;T:974183111;N:4416217,51,51,,,945319095,920831833,912749408,974183111,4416217,SRX12122770,SRS10102628,SRA1290854,GEO,Duke University School of Medicine,2,0.95901,0.9681,0.05957,0.05746,0.73614,0.73486,0.55063,0.55,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66029,SRR15831127,SRX12122770,SRS10102628,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 2,GSM5571383,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571383,GSM5571383: hnf4gCR 2; Danio rerio; RNA Seq,GSM5571383,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571383,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_6_hnf4gMut_S6_L002_R1_001.fastq.gz 110_6_hnf4gMut_S6_L002_R2_001.fastq.gz,fastq fastq,3863589252.0,37878326.0,GSM5571383 r2,0:51 1:51,A:971613305;C:948362761;G:938195739;T:1002960715;N:2456732,51,51,,,971613305,948362761,938195739,1002960715,2456732,SRX12122770,SRS10102628,SRA1290854,GEO,Duke University School of Medicine,2,0.96633,0.969,0.05911,0.05755,0.73267,0.73377,0.5546,0.54768,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66030,SRR15831124,SRX12122769,SRS10102629,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 1,GSM5571382,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571382,GSM5571382: hnf4gCR 1; Danio rerio; RNA Seq,GSM5571382,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571382,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_5_hnf4gMut_S5_L001_R1_001.fastq.gz 110_5_hnf4gMut_S5_L001_R2_001.fastq.gz,fastq fastq,4479974028.0,43921314.0,GSM5571382 r1,0:51 1:51,A:1119854063;C:1103072880;G:1094631404;T:1157150141;N:5265540,51,51,,,1119854063,1103072880,1094631404,1157150141,5265540,SRX12122769,SRS10102629,SRA1290854,GEO,Duke University School of Medicine,2,0.96069,0.96932,0.05524,0.05404,0.73214,0.73186,0.55212,0.54227,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66031,SRR15831125,SRX12122769,SRS10102629,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCR 1,GSM5571382,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,hnf4gCR 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionally rasied|age:6 dpf,GSM5571382,GSM5571382: hnf4gCR 1; Danio rerio; RNA Seq,GSM5571382,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571382,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_5_hnf4gMut_S5_L002_R1_001.fastq.gz 110_5_hnf4gMut_S5_L002_R2_001.fastq.gz,fastq fastq,4627550994.0,45368147.0,GSM5571382 r2,0:51 1:51,A:1156102135;C:1141260473;G:1130509685;T:1196742415;N:2936286,51,51,,,1156102135,1141260473,1130509685,1196742415,2936286,SRX12122769,SRS10102629,SRA1290854,GEO,Duke University School of Medicine,2,0.96658,0.96999,0.05728,0.05613,0.73243,0.73184,0.53606,0.54281,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66040,SRR15831114,SRX12122764,SRS10102623,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 4,GSM5571377,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571377,GSM5571377: hnf4gCV 4; Danio rerio; RNA Seq,GSM5571377,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571377,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S16_S16_L001_R1_001.fastq.gz 5872-S16_S16_L001_R2_001.fastq.gz,fastq fastq,2456031582.0,24078741.0,GSM5571377 r1,0:51 1:51,A:621856184;C:600456608;G:593979590;T:638943231;N:795969,51,51,,,621856184,600456608,593979590,638943231,795969,SRX12122764,SRS10102623,SRA1290854,GEO,Duke University School of Medicine,2,0.97,0.96545,0.06644,0.06345,0.72423,0.72462,0.53499,0.53491,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66041,SRR15831115,SRX12122764,SRS10102623,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 4,GSM5571377,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571377,GSM5571377: hnf4gCV 4; Danio rerio; RNA Seq,GSM5571377,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571377,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S16_S16_L002_R1_001.fastq.gz 5872-S16_S16_L002_R2_001.fastq.gz,fastq fastq,2468453856.0,24200528.0,GSM5571377 r2,0:51 1:51,A:624674624;C:603480964;G:595751715;T:642142386;N:2404167,51,51,,,624674624,603480964,595751715,642142386,2404167,SRX12122764,SRS10102623,SRA1290854,GEO,Duke University School of Medicine,2,0.9701,0.95989,0.06634,0.06287,0.7232,0.72387,0.54104,0.54855,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66042,SRR15831112,SRX12122763,SRS10102622,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 3,GSM5571376,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571376,GSM5571376: hnf4gCV 3; Danio rerio; RNA Seq,GSM5571376,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571376,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S12_S12_L001_R1_001.fastq.gz 5872-S12_S12_L001_R2_001.fastq.gz,fastq fastq,2467057068.0,24186834.0,GSM5571376 r1,0:51 1:51,A:619984451;C:608112264;G:599507543;T:638648345;N:804465,51,51,,,619984451,608112264,599507543,638648345,804465,SRX12122763,SRS10102622,SRA1290854,GEO,Duke University School of Medicine,2,0.97057,0.96527,0.07485,0.07132,0.71944,0.71954,0.55088,0.55863,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66043,SRR15831113,SRX12122763,SRS10102622,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 3,GSM5571376,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571376,GSM5571376: hnf4gCV 3; Danio rerio; RNA Seq,GSM5571376,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571376,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S12_S12_L002_R1_001.fastq.gz 5872-S12_S12_L002_R2_001.fastq.gz,fastq fastq,2481572382.0,24329141.0,GSM5571376 r2,0:51 1:51,A:623385209;C:611618540;G:601851951;T:642309402;N:2407280,51,51,,,623385209,611618540,601851951,642309402,2407280,SRX12122763,SRS10102622,SRA1290854,GEO,Duke University School of Medicine,2,0.97113,0.96078,0.07398,0.07147,0.71794,0.71912,0.55474,0.54499,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66044,SRR15831110,SRX12122762,SRS10102621,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 2,GSM5571375,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571375,GSM5571375: hnf4gCV 2; Danio rerio; RNA Seq,GSM5571375,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571375,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872_S19_S8_L001_R1_001.fastq.gz 5872_S19_S8_L001_R2_001.fastq.gz,fastq fastq,2652211038.0,26002069.0,GSM5571375 r1,0:51 1:51,A:666987614;C:655487534;G:646143545;T:682729344;N:863001,51,51,,,666987614,655487534,646143545,682729344,863001,SRX12122762,SRS10102621,SRA1290854,GEO,Duke University School of Medicine,2,0.97064,0.96564,0.07888,0.07577,0.73328,0.73444,0.53963,0.53954,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66045,SRR15831111,SRX12122762,SRS10102621,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 2,GSM5571375,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571375,GSM5571375: hnf4gCV 2; Danio rerio; RNA Seq,GSM5571375,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571375,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872_S19_S8_L002_R1_001.fastq.gz 5872_S19_S8_L002_R2_001.fastq.gz,fastq fastq,2668631202.0,26163051.0,GSM5571375 r2,0:51 1:51,A:670731749;C:659479750;G:648991850;T:686841727;N:2586126,51,51,,,670731749,659479750,648991850,686841727,2586126,SRX12122762,SRS10102621,SRA1290854,GEO,Duke University School of Medicine,2,0.97032,0.9595,0.0795,0.07552,0.73294,0.73425,0.54401,0.52776,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66046,SRR15831108,SRX12122761,SRS10102620,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 1,GSM5571374,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571374,GSM5571374: hnf4gCV 1; Danio rerio; RNA Seq,GSM5571374,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571374,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S4_S4_L001_R1_001.fastq.gz 5872-S4_S4_L001_R2_001.fastq.gz,fastq fastq,2731813776.0,26782488.0,GSM5571374 r1,0:51 1:51,A:682418510;C:680185287;G:669000806;T:699321892;N:887281,51,51,,,682418510,680185287,669000806,699321892,887281,SRX12122761,SRS10102620,SRA1290854,GEO,Duke University School of Medicine,2,0.97259,0.96604,0.08351,0.08017,0.73158,0.7317,0.55688,0.56714,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66047,SRR15831109,SRX12122761,SRS10102620,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gCV 1,GSM5571374,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,hnf4gCV 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571374,GSM5571374: hnf4gCV 1; Danio rerio; RNA Seq,GSM5571374,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571374,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S4_S4_L002_R1_001.fastq.gz 5872-S4_S4_L002_R2_001.fastq.gz,fastq fastq,2749135926.0,26952313.0,GSM5571374 r2,0:51 1:51,A:686565316;C:684275603;G:671888584;T:703741081;N:2665342,51,51,,,686565316,684275603,671888584,703741081,2665342,SRX12122761,SRS10102620,SRA1290854,GEO,Duke University School of Medicine,2,0.97194,0.96277,0.08345,0.08067,0.73054,0.73143,0.55603,0.55821,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66048,SRR15831106,SRX12122760,SRS10102619,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 4,GSM5571373,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571373,GSM5571373: WTCV 4; Danio rerio; RNA Seq,GSM5571373,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571373,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S15_S15_L001_R1_001.fastq.gz 5872-S15_S15_L001_R2_001.fastq.gz,fastq fastq,2458568628.0,24103614.0,GSM5571373 r1,0:51 1:51,A:621758603;C:603436782;G:592676389;T:639898440;N:798414,51,51,,,621758603,603436782,592676389,639898440,798414,SRX12122760,SRS10102619,SRA1290854,GEO,Duke University School of Medicine,2,0.96947,0.96468,0.07718,0.07473,0.72127,0.7223,0.55204,0.55952,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66049,SRR15831107,SRX12122760,SRS10102619,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 4,GSM5571373,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571373,GSM5571373: WTCV 4; Danio rerio; RNA Seq,GSM5571373,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571373,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S15_S15_L002_R1_001.fastq.gz 5872-S15_S15_L002_R2_001.fastq.gz,fastq fastq,2469415002.0,24209951.0,GSM5571373 r2,0:51 1:51,A:624230763;C:606027471;G:594177750;T:642584632;N:2394386,51,51,,,624230763,606027471,594177750,642584632,2394386,SRX12122760,SRS10102619,SRA1290854,GEO,Duke University School of Medicine,2,0.96997,0.95895,0.07801,0.0741,0.72312,0.7234,0.55892,0.55418,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66050,SRR15831104,SRX12122759,SRS10102618,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 3,GSM5571372,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571372,GSM5571372: WTCV 3; Danio rerio; RNA Seq,GSM5571372,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571372,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S11_S11_L001_R1_001.fastq.gz 5872-S11_S11_L001_R2_001.fastq.gz,fastq fastq,2624762634.0,25732967.0,GSM5571372 r1,0:51 1:51,A:659354074;C:649505839;G:638596142;T:676456669;N:849910,51,51,,,659354074,649505839,638596142,676456669,849910,SRX12122759,SRS10102618,SRA1290854,GEO,Duke University School of Medicine,2,0.97034,0.96513,0.07673,0.07265,0.71644,0.71681,0.56255,0.55631,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66051,SRR15831105,SRX12122759,SRS10102618,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 3,GSM5571372,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571372,GSM5571372: WTCV 3; Danio rerio; RNA Seq,GSM5571372,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571372,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S11_S11_L002_R1_001.fastq.gz 5872-S11_S11_L002_R2_001.fastq.gz,fastq fastq,2642645172.0,25908286.0,GSM5571372 r2,0:51 1:51,A:663616399;C:653770540;G:641680879;T:681013730;N:2563624,51,51,,,663616399,653770540,641680879,681013730,2563624,SRX12122759,SRS10102618,SRA1290854,GEO,Duke University School of Medicine,2,0.9713,0.96104,0.07642,0.07189,0.71644,0.71745,0.55529,0.55116,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66052,SRR15831102,SRX12122758,SRS10102616,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 2,GSM5571371,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571371,GSM5571371: WTCV 2; Danio rerio; RNA Seq,GSM5571371,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571371,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S7_S7_L001_R1_001.fastq.gz 5872-S7_S7_L001_R2_001.fastq.gz,fastq fastq,3209788530.0,31468515.0,GSM5571371 r1,0:51 1:51,A:806436616;C:790686982;G:783919913;T:827701839;N:1043180,51,51,,,806436616,790686982,783919913,827701839,1043180,SRX12122758,SRS10102616,SRA1290854,GEO,Duke University School of Medicine,2,0.97058,0.96565,0.07073,0.06717,0.73588,0.73568,0.53995,0.55216,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66053,SRR15831103,SRX12122758,SRS10102616,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 2,GSM5571371,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571371,GSM5571371: WTCV 2; Danio rerio; RNA Seq,GSM5571371,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571371,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S7_S7_L002_R1_001.fastq.gz 5872-S7_S7_L002_R2_001.fastq.gz,fastq fastq,3239942382.0,31764141.0,GSM5571371 r2,0:51 1:51,A:813599395;C:797986648;G:789755474;T:835446494;N:3154371,51,51,,,813599395,797986648,789755474,835446494,3154371,SRX12122758,SRS10102616,SRA1290854,GEO,Duke University School of Medicine,2,0.97112,0.96194,0.07013,0.06688,0.7347,0.73659,0.55379,0.52497,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66054,SRR15831100,SRX12122757,SRS10102617,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 1,GSM5571370,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571370,GSM5571370: WTCV 1; Danio rerio; RNA Seq,GSM5571370,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571370,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S3_S3_L001_R1_001.fastq.gz 5872-S3_S3_L001_R2_001.fastq.gz,fastq fastq,2148352152.0,21062276.0,GSM5571370 r1,0:51 1:51,A:545847865;C:524880749;G:517895424;T:559029412;N:698702,51,51,,,545847865,524880749,517895424,559029412,698702,SRX12122757,SRS10102617,SRA1290854,GEO,Duke University School of Medicine,2,0.9696,0.96439,0.07002,0.06658,0.71293,0.71382,0.53237,0.5425,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66055,SRR15831101,SRX12122757,SRS10102617,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCV 1,GSM5571370,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,WTCV 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf,GSM5571370,GSM5571370: WTCV 1; Danio rerio; RNA Seq,GSM5571370,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571370,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S3_S3_L002_R1_001.fastq.gz 5872-S3_S3_L002_R2_001.fastq.gz,fastq fastq,2164713768.0,21222684.0,GSM5571370 r2,0:51 1:51,A:549705820;C:528796940;G:520784980;T:563315850;N:2110178,51,51,,,549705820,528796940,520784980,563315850,2110178,SRX12122757,SRS10102617,SRA1290854,GEO,Duke University School of Medicine,2,0.97022,0.95926,0.06991,0.06634,0.71261,0.71273,0.53411,0.53711,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66056,SRR15831098,SRX12122756,SRS10102615,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 4,GSM5571369,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571369,GSM5571369: hnf4gGF 4; Danio rerio; RNA Seq,GSM5571369,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571369,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S14_S14_L001_R1_001.fastq.gz 5872-S14_S14_L001_R2_001.fastq.gz,fastq fastq,2835903348.0,27802974.0,GSM5571369 r1,0:51 1:51,A:709443116;C:700805533;G:693682503;T:731054666;N:917530,51,51,,,709443116,700805533,693682503,731054666,917530,SRX12122756,SRS10102615,SRA1290854,GEO,Duke University School of Medicine,2,0.97221,0.96737,0.06186,0.05922,0.73509,0.73531,0.55074,0.54822,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66057,SRR15831099,SRX12122756,SRS10102615,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 4,GSM5571369,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571369,GSM5571369: hnf4gGF 4; Danio rerio; RNA Seq,GSM5571369,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571369,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S14_S14_L002_R1_001.fastq.gz 5872-S14_S14_L002_R2_001.fastq.gz,fastq fastq,2854893198.0,27989149.0,GSM5571369 r2,0:51 1:51,A:713854963;C:705281866;G:697150130;T:735809931;N:2796308,51,51,,,713854963,705281866,697150130,735809931,2796308,SRX12122756,SRS10102615,SRA1290854,GEO,Duke University School of Medicine,2,0.97233,0.96283,0.0626,0.05924,0.73452,0.73513,0.55144,0.55421,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66058,SRR15831096,SRX12122755,SRS10102614,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 3,GSM5571368,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571368,GSM5571368: hnf4gGF 3; Danio rerio; RNA Seq,GSM5571368,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571368,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S10_S10_L001_R1_001.fastq.gz 5872-S10_S10_L001_R2_001.fastq.gz,fastq fastq,2357187462.0,23109681.0,GSM5571368 r1,0:51 1:51,A:586366022;C:589008970;G:578250815;T:602798178;N:763477,51,51,,,586366022,589008970,578250815,602798178,763477,SRX12122755,SRS10102614,SRA1290854,GEO,Duke University School of Medicine,2,0.97392,0.96757,0.06832,0.0653,0.73105,0.73158,0.54666,0.54277,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66059,SRR15831097,SRX12122755,SRS10102614,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 3,GSM5571368,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571368,GSM5571368: hnf4gGF 3; Danio rerio; RNA Seq,GSM5571368,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571368,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S10_S10_L002_R1_001.fastq.gz 5872-S10_S10_L002_R2_001.fastq.gz,fastq fastq,2374022766.0,23274733.0,GSM5571368 r2,0:51 1:51,A:590229930;C:593090956;G:581277183;T:607112573;N:2312124,51,51,,,590229930,593090956,581277183,607112573,2312124,SRX12122755,SRS10102614,SRA1290854,GEO,Duke University School of Medicine,2,0.97435,0.96256,0.06859,0.06565,0.73022,0.73133,0.5224,0.54342,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66060,SRR15831094,SRX12122754,SRS10102612,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 2,GSM5571367,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571367,GSM5571367: hnf4gGF 2; Danio rerio; RNA Seq,GSM5571367,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571367,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S6_S6_L001_R1_001.fastq.gz 5872-S6_S6_L001_R2_001.fastq.gz,fastq fastq,2481292698.0,24326399.0,GSM5571367 r1,0:51 1:51,A:623595282;C:613642686;G:605734258;T:637513641;N:806831,51,51,,,623595282,613642686,605734258,637513641,806831,SRX12122754,SRS10102612,SRA1290854,GEO,Duke University School of Medicine,2,0.97355,0.96795,0.06312,0.06079,0.7497,0.75,0.54929,0.54592,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66061,SRR15831095,SRX12122754,SRS10102612,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 2,GSM5571367,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571367,GSM5571367: hnf4gGF 2; Danio rerio; RNA Seq,GSM5571367,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571367,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S6_S6_L002_R1_001.fastq.gz 5872-S6_S6_L002_R2_001.fastq.gz,fastq fastq,2495586570.0,24466535.0,GSM5571367 r2,0:51 1:51,A:626740336;C:617142817;G:608194088;T:641090696;N:2418633,51,51,,,626740336,617142817,608194088,641090696,2418633,SRX12122754,SRS10102612,SRA1290854,GEO,Duke University School of Medicine,2,0.97341,0.96303,0.06357,0.06086,0.74801,0.74953,0.54947,0.53539,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66062,SRR15831092,SRX12122753,SRS10102611,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 1,GSM5571366,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571366,GSM5571366: hnf4gGF 1; Danio rerio; RNA Seq,GSM5571366,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571366,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S2_S2_L001_R1_001.fastq.gz 5872-S2_S2_L001_R2_001.fastq.gz,fastq fastq,2478252384.0,24296592.0,GSM5571366 r1,0:51 1:51,A:628840310;C:606575096;G:598426644;T:643602224;N:808110,51,51,,,628840310,606575096,598426644,643602224,808110,SRX12122753,SRS10102611,SRA1290854,GEO,Duke University School of Medicine,2,0.96963,0.96422,0.07528,0.07146,0.71938,0.71961,0.54488,0.54591,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66063,SRR15831093,SRX12122753,SRS10102611,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,hnf4gGF 1,GSM5571366,,source name:dissected GI tract|tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,hnf4gGF 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:hnf4g / |microbial status:Germfree|age:6 dpf,GSM5571366,GSM5571366: hnf4gGF 1; Danio rerio; RNA Seq,GSM5571366,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571366,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S2_S2_L002_R1_001.fastq.gz 5872-S2_S2_L002_R2_001.fastq.gz,fastq fastq,2466734748.0,24183674.0,GSM5571366 r2,0:51 1:51,A:625574739;C:603606213;G:594449200;T:640734998;N:2369598,51,51,,,625574739,603606213,594449200,640734998,2369598,SRX12122753,SRS10102611,SRA1290854,GEO,Duke University School of Medicine,2,0.9704,0.95977,0.07355,0.06973,0.72011,0.72046,0.54423,0.55225,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66064,SRR15831090,SRX12122752,SRS10102613,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 4,GSM5571365,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571365,GSM5571365: WTGF 4; Danio rerio; RNA Seq,GSM5571365,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571365,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S13_S13_L001_R1_001.fastq.gz 5872-S13_S13_L001_R2_001.fastq.gz,fastq fastq,2328762612.0,22831006.0,GSM5571365 r1,0:51 1:51,A:583874072;C:577838306;G:568940852;T:597352003;N:757379,51,51,,,583874072,577838306,568940852,597352003,757379,SRX12122752,SRS10102613,SRA1290854,GEO,Duke University School of Medicine,2,0.97396,0.96792,0.06956,0.06554,0.72626,0.72634,0.54885,0.55812,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66065,SRR15831091,SRX12122752,SRS10102613,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 4,GSM5571365,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571365,GSM5571365: WTGF 4; Danio rerio; RNA Seq,GSM5571365,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571365,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S13_S13_L002_R1_001.fastq.gz 5872-S13_S13_L002_R2_001.fastq.gz,fastq fastq,2344934610.0,22989555.0,GSM5571365 r2,0:51 1:51,A:587685701;C:581688570;G:571736834;T:601542111;N:2281394,51,51,,,587685701,581688570,571736834,601542111,2281394,SRX12122752,SRS10102613,SRA1290854,GEO,Duke University School of Medicine,2,0.97384,0.96376,0.07016,0.06622,0.72521,0.72669,0.55308,0.54718,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66066,SRR15831088,SRX12122751,SRS10102610,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 3,GSM5571364,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571364,GSM5571364: WTGF 3; Danio rerio; RNA Seq,GSM5571364,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571364,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S9_S9_L001_R1_001.fastq.gz 5872-S9_S9_L001_R2_001.fastq.gz,fastq fastq,2633554218.0,25819159.0,GSM5571364 r1,0:51 1:51,A:663526823;C:646724857;G:640621642;T:681821680;N:859216,51,51,,,663526823,646724857,640621642,681821680,859216,SRX12122751,SRS10102610,SRA1290854,GEO,Duke University School of Medicine,2,0.97194,0.96643,0.06591,0.06254,0.72896,0.7301,0.55541,0.55009,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66067,SRR15831089,SRX12122751,SRS10102610,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 3,GSM5571364,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571364,GSM5571364: WTGF 3; Danio rerio; RNA Seq,GSM5571364,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571364,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S9_S9_L002_R1_001.fastq.gz 5872-S9_S9_L002_R2_001.fastq.gz,fastq fastq,2631071436.0,25794818.0,GSM5571364 r2,0:51 1:51,A:662549092;C:646093782;G:638818105;T:681061525;N:2548932,51,51,,,662549092,646093782,638818105,681061525,2548932,SRX12122751,SRS10102610,SRA1290854,GEO,Duke University School of Medicine,2,0.97164,0.96139,0.06576,0.06178,0.72985,0.73267,0.55311,0.54864,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66068,SRR15831086,SRX12122750,SRS10102609,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 2,GSM5571363,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571363,GSM5571363: WTGF 2; Danio rerio; RNA Seq,GSM5571363,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571363,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S5_S5_L001_R1_001.fastq.gz 5872-S5_S5_L001_R2_001.fastq.gz,fastq fastq,3004672038.0,29457569.0,GSM5571363 r1,0:51 1:51,A:753701649;C:744846750;G:733477640;T:771669814;N:976185,51,51,,,753701649,744846750,733477640,771669814,976185,SRX12122750,SRS10102609,SRA1290854,GEO,Duke University School of Medicine,2,0.97169,0.96588,0.07922,0.07597,0.7376,0.73795,0.56909,0.56237,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66069,SRR15831087,SRX12122750,SRS10102609,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 2,GSM5571363,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571363,GSM5571363: WTGF 2; Danio rerio; RNA Seq,GSM5571363,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571363,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S5_S5_L002_R1_001.fastq.gz 5872-S5_S5_L002_R2_001.fastq.gz,fastq fastq,3024802452.0,29654926.0,GSM5571363 r2,0:51 1:51,A:758352092;C:749757338;G:736930864;T:776827549;N:2934609,51,51,,,758352092,749757338,736930864,776827549,2934609,SRX12122750,SRS10102609,SRA1290854,GEO,Duke University School of Medicine,2,0.97206,0.96163,0.07982,0.0758,0.73472,0.73492,0.55837,0.55682,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66070,SRR15831084,SRX12122749,SRS10102608,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 1,GSM5571362,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571362,GSM5571362: WTGF 1; Danio rerio; RNA Seq,GSM5571362,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571362,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S1_S1_L001_R1_001.fastq.gz 5872-S1_S1_L001_R2_001.fastq.gz,fastq fastq,3439748856.0,33723028.0,GSM5571362 r1,0:51 1:51,A:867376368;C:842804400;G:836101030;T:892353191;N:1113867,51,51,,,867376368,842804400,836101030,892353191,1113867,SRX12122749,SRS10102608,SRA1290854,GEO,Duke University School of Medicine,2,0.96892,0.9643,0.07175,0.06904,0.73389,0.73458,0.53485,0.53714,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System
66071,SRR15831085,SRX12122749,SRS10102608,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTGF 1,GSM5571362,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,WTGF 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Germfree|age:6 dpf,GSM5571362,GSM5571362: WTGF 1; Danio rerio; RNA Seq,GSM5571362,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571362,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,5872-S1_S1_L002_R1_001.fastq.gz 5872-S1_S1_L002_R2_001.fastq.gz,fastq fastq,3461934570.0,33940535.0,GSM5571362 r2,0:51 1:51,A:872518731;C:848059273;G:839894344;T:898100395;N:3361827,51,51,,,872518731,848059273,839894344,898100395,3361827,SRX12122749,SRS10102608,SRA1290854,GEO,Duke University School of Medicine,2,0.97023,0.96129,0.07269,0.06843,0.73389,0.73413,0.53362,0.55743,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Gut,Digestive System