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 29041,SRR26990794,SRX22683825,SRS19677539,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut3,GSM7924158,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924158,GSM7924158: WT gut3; Danio rerio; RNA Seq,GSM7924158 r1,GSM7924158,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz,fastq fastq,6066709786.0,20088443.0,GSM7924158 r1,0:151 1:151,A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156,151,151,,,1673762656,1360901090,1385125931,1646863953,56156,SRX22683825,SRS19677539,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.92515,0.9297,0.0691,0.0659,0.75041,0.75022,0.53007,0.53064,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System 29042,SRR26990795,SRX22683824,SRS19677538,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut2,GSM7924157,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924157,GSM7924157: WT gut2; Danio rerio; RNA Seq,GSM7924157 r1,GSM7924157,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz,fastq fastq,5406867570.0,17903535.0,GSM7924157 r1,0:151 1:151,A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612,151,151,,,1464846243,1237183908,1259215309,1445572498,49612,SRX22683824,SRS19677538,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93795,0.94322,0.05952,0.05592,0.75933,0.75887,0.54179,0.53451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System 29043,SRR26990796,SRX22683823,SRS19677537,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut1,GSM7924156,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924156,GSM7924156: WT gut1; Danio rerio; RNA Seq,GSM7924156 r1,GSM7924156,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz,fastq fastq,5162192908.0,17093354.0,GSM7924156 r1,0:151 1:151,A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343,151,151,,,1404682153,1175657030,1196829496,1384975886,48343,SRX22683823,SRS19677537,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93119,0.93585,0.06122,0.05809,0.74757,0.74757,0.54124,0.54417,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System 29044,SRR26990797,SRX22683822,SRS19677536,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut3,GSM7924155,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924155,GSM7924155: itgavKO gut3; Danio rerio; RNA Seq,GSM7924155 r1,GSM7924155,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz,fastq fastq,4146743578.0,13730939.0,GSM7924155 r1,0:151 1:151,A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387,151,151,,,1130002132,943522869,958031732,1115146458,40387,SRX22683822,SRS19677536,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93764,0.94144,0.05938,0.05594,0.7553,0.75485,0.55535,0.55018,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System 29045,SRR26990798,SRX22683821,SRS19677535,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut2,GSM7924154,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924154,GSM7924154: itgavKO gut2; Danio rerio; RNA Seq,GSM7924154 r1,GSM7924154,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz,fastq fastq,4225756140.0,13992570.0,GSM7924154 r1,0:151 1:151,A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530,151,151,,,1133211420,974497998,995876972,1122129220,40530,SRX22683821,SRS19677535,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.95341,0.95884,0.05109,0.04883,0.77542,0.77368,0.51301,0.50704,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System 29046,SRR26990799,SRX22683820,SRS19677534,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itagvKO gut1,GSM7924153,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itagvKO gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924153,GSM7924153: itagvKO gut1; Danio rerio; RNA Seq,GSM7924153 r1,GSM7924153,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz,fastq fastq,5954117844.0,19715622.0,GSM7924153 r1,0:151 1:151,A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859,151,151,,,1600496071,1372939932,1393534700,1587094282,52859,SRX22683820,SRS19677534,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.94807,0.95298,0.05682,0.05385,0.74004,0.73925,0.54423,0.54484,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System 55495,SRR10511896,SRX7200010,SRS5705565,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta2Gut2,GSM4187022,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2,3dpRSta2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2|age dpf = dpf,GSM4187022,GSM4187022: 3dpRSta2Gut2; Danio rerio; RNA Seq,GSM4187022,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_27_concat_R1.fastq.gz,fastq,1397453550.0,27401050.0,GSM4187022 r1,0:51 1:0,A:409993093;C:286631833;G:275766237;T:425009393;N:52994,51,0,,,409993093,286631833,275766237,425009393,52994,SRX7200010,SRS5705565,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9238,,0.127,,0.74718,,0.55171,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55496,SRR10511895,SRX7200009,SRS5705564,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta2Gut1,GSM4187021,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2,3dpRSta2Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 2|age dpf = dpf,GSM4187021,GSM4187021: 3dpRSta2Gut1; Danio rerio; RNA Seq,GSM4187021,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_23_concat_R1.fastq.gz,fastq,1571369211.0,30811161.0,GSM4187021 r1,0:51 1:0,A:451585039;C:329412420;G:316009619;T:474302622;N:59511,51,0,,,451585039,329412420,316009619,474302622,59511,SRX7200009,SRS5705564,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.92047,,0.12142,,0.74785,,0.56011,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55497,SRR10511894,SRX7200008,SRS5705563,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta1Gut3,GSM4187020,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1,3dpRSta1Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1|age dpf = dpf,GSM4187020,GSM4187020: 3dpRSta1Gut3; Danio rerio; RNA Seq,GSM4187020,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_22_concat_R1.fastq.gz,fastq,1473918717.0,28900367.0,GSM4187020 r1,0:51 1:0,A:422349451;C:308266246;G:300748378;T:442499660;N:54982,51,0,,,422349451,308266246,300748378,442499660,54982,SRX7200008,SRS5705563,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93232,,0.10841,,0.7573,,0.53817,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55498,SRR10511893,SRX7200007,SRS5705562,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRSta1Gut1,GSM4187019,,source name:Intestine|tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1,3dpRSta1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved Refed at 21 days|tank:Starved tank 1|age dpf = dpf,GSM4187019,GSM4187019: 3dpRSta1Gut1; Danio rerio; RNA Seq,GSM4187019,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_21_concat_R1.fastq.gz,fastq,1551630273.0,30424123.0,GSM4187019 r1,0:51 1:0,A:451110725;C:322314892;G:308247205;T:469898838;N:58613,51,0,,,451110725,322314892,308247205,469898838,58613,SRX7200007,SRS5705562,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9272,,0.11972,,0.75822,,0.54861,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55499,SRR10511892,SRX7200006,SRS5705561,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed2Gut3,GSM4187018,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpRFed2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187018,GSM4187018: 3dpRFed2Gut3; Danio rerio; RNA Seq,GSM4187018,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_20_concat_R1.fastq.gz,fastq,1429183557.0,28023207.0,GSM4187018 r1,0:51 1:0,A:406259184;C:299540462;G:297537630;T:425792267;N:54014,51,0,,,406259184,299540462,297537630,425792267,54014,SRX7200006,SRS5705561,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93776,,0.10446,,0.75659,,0.51357,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55500,SRR10511891,SRX7200005,SRS5705560,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed2Gut2,GSM4187017,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpRFed2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187017,GSM4187017: 3dpRFed2Gut2; Danio rerio; RNA Seq,GSM4187017,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_19_concat_R1.fastq.gz,fastq,1766365875.0,34634625.0,GSM4187017 r1,0:51 1:0,A:499095968;C:376678270;G:363861124;T:526664286;N:66227,51,0,,,499095968,376678270,363861124,526664286,66227,SRX7200005,SRS5705560,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93356,,0.10506,,0.75812,,0.54405,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55501,SRR10511882,SRX7200004,SRS5705559,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSFed1Gut3,GSM4187008,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,21dpSFed1Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187008,GSM4187008: 21dpSFed1Gut3; Danio rerio; RNA Seq,GSM4187008,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187008,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_10_concat_R1.fastq.gz,fastq,1592532834.0,31226134.0,GSM4187008 r1,0:51 1:0,A:429617322;C:351337972;G:347154272;T:464366202;N:57066,51,0,,,429617322,351337972,347154272,464366202,57066,SRX7200004,SRS5705559,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93898,,0.09149,,0.75568,,0.51578,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55502,SRR10511881,SRX7200003,SRS5705558,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSFed1Gut1,GSM4187007,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,21dpSFed1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187007,GSM4187007: 21dpSFed1Gut1; Danio rerio; RNA Seq,GSM4187007,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187007,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_9_concat_R1.fastq.gz,fastq,1575514695.0,30892445.0,GSM4187007 r1,0:51 1:0,A:441324595;C:335749891;G:331699440;T:466684268;N:56501,51,0,,,441324595,335749891,331699440,466684268,56501,SRX7200003,SRS5705558,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93304,,0.11059,,0.75286,,0.55511,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55503,SRR10511880,SRX7200002,SRS5705557,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta2Gut3,GSM4187006,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,3dpSSta2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187006,GSM4187006: 3dpSSta2Gut3; Danio rerio; RNA Seq,GSM4187006,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187006,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_8_concat_R1.fastq.gz,fastq,1785917949.0,35017999.0,GSM4187006 r1,0:51 1:0,A:509554159;C:377147211;G:365503374;T:533656366;N:56839,51,0,,,509554159,377147211,365503374,533656366,56839,SRX7200002,SRS5705557,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93641,,0.11479,,0.75351,,0.53275,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55504,SRR10511879,SRX7200001,SRS5705556,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta2Gut2,GSM4187005,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,3dpSSta2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187005,GSM4187005: 3dpSSta2Gut2; Danio rerio; RNA Seq,GSM4187005,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187005,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_7_concat_R1.fastq.gz,fastq,1789874325.0,35095575.0,GSM4187005 r1,0:51 1:0,A:495592326;C:391304311;G:373137484;T:529784276;N:55928,51,0,,,495592326,391304311,373137484,529784276,55928,SRX7200001,SRS5705556,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9421,,0.1111,,0.74566,,0.54158,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55505,SRR10511878,SRX7200000,SRS5705555,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta1Gut2,GSM4187004,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 1,3dpSSta1Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 1|age dpf = dpf,GSM4187004,GSM4187004: 3dpSSta1Gut2; Danio rerio; RNA Seq,GSM4187004,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187004,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_6_concat_R1.fastq.gz,fastq,1641362580.0,32183580.0,GSM4187004 r1,0:51 1:0,A:483646499;C:336487643;G:323951194;T:497225233;N:52011,51,0,,,483646499,336487643,323951194,497225233,52011,SRX7200000,SRS5705555,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.9344,,0.13244,,0.74734,,0.52964,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55506,SRR10511877,SRX7199999,SRS5705554,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSSta1Gut1,GSM4187003,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 1,3dpSSta1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 1|age dpf = dpf,GSM4187003,GSM4187003: 3dpSSta1Gut1; Danio rerio; RNA Seq,GSM4187003,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187003,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_5_concat_R1.fastq.gz,fastq,1571663532.0,30816932.0,GSM4187003 r1,0:51 1:0,A:454772545;C:325458319;G:321434801;T:469947006;N:50861,51,0,,,454772545,325458319,321434801,469947006,50861,SRX7199999,SRS5705554,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93659,,0.11683,,0.75213,,0.52836,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55507,SRR10511876,SRX7199998,SRS5705553,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSFed2Gut3,GSM4187002,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpSFed2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187002,GSM4187002: 3dpSFed2Gut3; Danio rerio; RNA Seq,GSM4187002,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187002,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_4_concat_R1.fastq.gz,fastq,1561236174.0,30612474.0,GSM4187002 r1,0:51 1:0,A:467439399;C:310187678;G:304525609;T:479032805;N:50683,51,0,,,467439399,310187678,304525609,479032805,50683,SRX7199998,SRS5705553,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93358,,0.14283,,0.74939,,0.56013,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55508,SRR10511875,SRX7199997,SRS5705552,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSFed2Gut2,GSM4187001,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,3dpSFed2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187001,GSM4187001: 3dpSFed2Gut2; Danio rerio; RNA Seq,GSM4187001,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187001,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_3_concat_R1.fastq.gz,fastq,1927545255.0,37795005.0,GSM4187001 r1,0:51 1:0,A:567770670;C:395455630;G:379200223;T:585057600;N:61132,51,0,,,567770670,395455630,379200223,585057600,61132,SRX7199997,SRS5705552,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93207,,0.13563,,0.75144,,0.54701,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55509,SRR10511890,SRX7199996,SRS5705551,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed1Gut3,GSM4187016,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,3dpRFed1Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187016,GSM4187016: 3dpRFed1Gut3; Danio rerio; RNA Seq,GSM4187016,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187016,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_18_concat_R1.fastq.gz,fastq,1733200167.0,33984317.0,GSM4187016 r1,0:51 1:0,A:478883149;C:377608593;G:368322683;T:508321013;N:64729,51,0,,,478883149,377608593,368322683,508321013,64729,SRX7199996,SRS5705551,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93695,,0.09593,,0.75341,,0.55416,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55510,SRR10511889,SRX7199995,SRS5705550,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpRFed1Gut2,GSM4187015,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,3dpRFed1Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187015,GSM4187015: 3dpRFed1Gut2; Danio rerio; RNA Seq,GSM4187015,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187015,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_17_concat_R1.fastq.gz,fastq,1639139490.0,32139990.0,GSM4187015 r1,0:51 1:0,A:472266921;C:343820482;G:331431433;T:491557290;N:63364,51,0,,,472266921,343820482,331431433,491557290,63364,SRX7199995,SRS5705550,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.92641,,0.11798,,0.74614,,0.55037,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55511,SRR10511888,SRX7199994,SRS5705549,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSSta2Gut3,GSM4187014,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,21dpSSta2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187014,GSM4187014: 21dpSSta2Gut3; Danio rerio; RNA Seq,GSM4187014,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187014,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_28_concat_R1.fastq,fastq,1957248165.0,38377415.0,GSM4187014 r1,0:51 1:0,A:568790177;C:410992982;G:388696297;T:588697675;N:71034,51,0,,,568790177,410992982,388696297,588697675,71034,SRX7199994,SRS5705549,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.937,,0.12586,,0.75921,,0.53627,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55512,SRR10511887,SRX7199993,SRS5705548,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSSta2Gut2,GSM4187013,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,21dpSSta2Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187013,GSM4187013: 21dpSSta2Gut2; Danio rerio; RNA Seq,GSM4187013,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187013,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_16_concat_R1.fastq.gz,fastq,1722397500.0,33772500.0,GSM4187013 r1,0:51 1:0,A:483227292;C:368630214;G:361368304;T:509108986;N:62704,51,0,,,483227292,368630214,361368304,509108986,62704,SRX7199993,SRS5705548,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.94065,,0.11314,,0.73726,,0.53094,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55513,SRR10511886,SRX7199992,SRS5705547,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpsSta2Gut1,GSM4187012,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 2,21dpsSta2Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 2|age dpf = dpf,GSM4187012,GSM4187012: 21dpsSta2Gut1; Danio rerio; RNA Seq,GSM4187012,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187012,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_15_concat_R1.fastq.gz,fastq,1883046633.0,36922483.0,GSM4187012 r1,0:51 1:0,A:535885753;C:401729105;G:382301792;T:563061958;N:68025,51,0,,,535885753,401729105,382301792,563061958,68025,SRX7199992,SRS5705547,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.94161,,0.11585,,0.74848,,0.50594,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55514,SRR10511885,SRX7199991,SRS5705546,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSSta1Gut2,GSM4187011,,source name:Intestine|tissue:Intestine|treatment:Starved|tank:Starved tank 1,21dpSSta1Gut2,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Starved|tank:Starved tank 1|age dpf = dpf,GSM4187011,GSM4187011: 21dpSSta1Gut2; Danio rerio; RNA Seq,GSM4187011,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187011,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_14_concat_R1.fastq.gz,fastq,1810471950.0,35499450.0,GSM4187011 r1,0:51 1:0,A:515524495;C:386623119;G:369300060;T:538958945;N:65331,51,0,,,515524495,386623119,369300060,538958945,65331,SRX7199991,SRS5705546,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93788,,0.1201,,0.73576,,0.536,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55515,SRR10511884,SRX7199990,SRS5705545,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpSFed2Gut3,GSM4187010,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,21dpSFed2Gut3,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187010,GSM4187010: 21dpSFed2Gut3; Danio rerio; RNA Seq,GSM4187010,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187010,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_12_concat_R1.fastq.gz,fastq,1594835535.0,31271285.0,GSM4187010 r1,0:51 1:0,A:456360065;C:335880726;G:319279080;T:483257577;N:58087,51,0,,,456360065,335880726,319279080,483257577,58087,SRX7199990,SRS5705545,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.935,,0.11846,,0.7556,,0.54994,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55516,SRR10511883,SRX7199989,SRS5705544,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,21dpsFed2Gut1,GSM4187009,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2,21dpsFed2Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 2|age dpf = dpf,GSM4187009,GSM4187009: 21dpsFed2Gut1; Danio rerio; RNA Seq,GSM4187009,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187009,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_11_concat_R1.fastq.gz,fastq,1657780041.0,32505491.0,GSM4187009 r1,0:51 1:0,A:467924183;C:353835126;G:340667908;T:495293545;N:59279,51,0,,,467924183,353835126,340667908,495293545,59279,SRX7199989,SRS5705544,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.93452,,0.1059,,0.75897,,0.56316,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System 55517,SRR10511874,SRX7199988,SRS5705543,SRP231178,PRJNA591019,Gene expression in the adult zebrafish intestine during starvation and refeeding,GSE140821,Transcriptome Analysis,In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.,,pubmed:35317738,,3dpSFed1Gut1,GSM4187000,,source name:Intestine|tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1,3dpSFed1Gut1,Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10,Intestine,,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.,tissue:Intestine|treatment:Continuously fed|tank:Fed tank 1|age dpf = dpf,GSM4187000,GSM4187000: 3dpSFed1Gut1; Danio rerio; RNA Seq,GSM4187000,,1,Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.,GEO Accession:GSM4187000,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP231178,,,SC_1_concat_R1.fastq.gz,fastq,1579970973.0,30979823.0,GSM4187000 r1,0:51 1:0,A:438395339;C:340541415;G:338487129;T:462497338;N:49752,51,0,,,438395339,340541415,338487129,462497338,49752,SRX7199988,SRS5705543,SRA1000332,GEO,"Molecular Genetics and Microbiology, Duke University",1,0.94225,,0.09616,,0.76021,,0.53717,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2019-11-21,Multi-stage,Multi-stage,Gut,Digestive System