{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"unknown\" and tissue_curation_coarse = \"Digestive System\"", "rows": [[32, "DRR408242", "DRX393848", "DRS407006", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB adult gut replicate 3", "zebrafish adult gut replicate 3", "SAMD00529462", null, "sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529462", "DRX393848", "AR019 gut 6  adult", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529462", null, null, null, 3546347364.0, 28145614.0, "DRR408242", "0:126 1:0", "A:919466631;C:829424335;G:818581155;T:978810217;N:65026", 126, 0, null, null, 919466631, 829424335, 818581155, 978810217, 65026, "DRX393848", "DRS407006", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Adult", "Adult", "Gut", "Digestive System"], [33, "DRR408241", "DRX393847", "DRS407005", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB adult gut replicate 2", "zebrafish adult gut replicate 2", "SAMD00529461", null, "sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529461", "DRX393847", "AR006 gut 4  adult", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529461", null, null, null, 3671973648.0, 29142648.0, "DRR408241", "0:126 1:0", "A:942167543;C:859431290;G:852661772;T:1017643011;N:70032", 126, 0, null, null, 942167543, 859431290, 852661772, 1017643011, 70032, "DRX393847", "DRS407005", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Adult", "Adult", "Gut", "Digestive System"], [34, "DRR408240", "DRX393846", "DRS407004", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB adult gut replicate 1", "zebrafish adult gut replicate 1", "SAMD00529460", null, "sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529460", "DRX393846", "AR004 gut 2  adult", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529460", null, null, null, 3480523704.0, 27623204.0, "DRR408240", "0:126 1:0", "A:898051986;C:827557593;G:816541244;T:938307607;N:65274", 126, 0, null, null, 898051986, 827557593, 816541244, 938307607, 65274, "DRX393846", "DRS407004", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Adult", "Adult", "Gut", "Digestive System"], [35, "DRR408239", "DRX393845", "DRS407003", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB larval gut replicate 3", "zebrafish larval gut replicate 3", "SAMD00529459", null, "sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529459", "DRX393845", "AR012 gut 5  5 dpf 6 dpf larvae", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529459", null, null, null, 3463982046.0, 27491921.0, "DRR408239", "0:126 1:0", "A:842552557;C:849757648;G:837664725;T:933942026;N:65090", 126, 0, null, null, 842552557, 849757648, 837664725, 933942026, 65090, "DRX393845", "DRS407003", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Larval", "Larval", "Gut", "Digestive System"], [36, "DRR408238", "DRX393844", "DRS407002", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB larval gut replicate 2", "zebrafish larval gut replicate 2", "SAMD00529458", null, "sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529458", "DRX393844", "AR005 gut 3  5 dpf 6 dpf larvae", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529458", null, null, null, 3782320416.0, 30018416.0, "DRR408238", "0:126 1:0", "A:930337206;C:920645770;G:906559955;T:1024704277;N:73208", 126, 0, null, null, 930337206, 920645770, 906559955, 1024704277, 73208, "DRX393844", "DRS407002", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Larval", "Larval", "Gut", "Digestive System"], [37, "DRR408237", "DRX393843", "DRS407001", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB larval gut replicate 1", "zebrafish larval gut replicate 1", "SAMD00529457", null, "sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529457", "DRX393843", "AR002 gut 1  5 dpf 6 dpf larvae", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529457", null, null, null, 3606885828.0, 28626078.0, "DRR408237", "0:126 1:0", "A:879148446;C:885673723;G:870330963;T:971663212;N:69484", 126, 0, null, null, 879148446, 885673723, 870330963, 971663212, 69484, "DRX393843", "DRS407001", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Larval", "Larval", "Gut", "Digestive System"], [172, "DRR075398", "DRX069312", "DRS075493", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The gut of control fish 7dpf", "Control gut", "SAMD00065412", null, "sample name:2 control gut 150701 Hiseq3A l3 018|tissue type:Gut", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065412", "DRX069312", "Control gut", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065412", null, null, null, 1008093492.0, 28002597.0, "DRR075398", "0:36", "A:230431417;C:251640901;G:244174255;T:281811580;N:35339", 36, null, null, null, 230431417, 251640901, 244174255, 281811580, 35339, "DRX069312", "DRS075493", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.9173, null, 0.07181, null, 0.72017, null, 0.45193, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Gut", "Digestive System"], [38009, "SRR1265748", "SRX529142", "SRS598839", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Gut Replicate 3 sRNAseq", "GSM1376631", null, "source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type   Singapore strain", "Female Gut Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Gut", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Gut|genetic background:Wild type   Singapore strain", "GSM1376631", "GSM1376631: Female Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376631", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376631", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZG012_TTAGGC_L008_R1.fastq.gz", "fastq", 425902173.0, 8351023.0, "GSM1376631 r1", "0:51", "A:85733692;C:98728458;G:130104130;T:111282282;N:53611", 51, null, null, null, 85733692, 98728458, 130104130, 111282282, 53611, "SRX529142", "SRS598839", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00598, null, 0.00074, null, 0.99565, null, 0.68818, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gut", "Digestive System"], [38010, "SRR1265747", "SRX529141", "SRS598838", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Gut Replicate 2 sRNAseq", "GSM1376630", null, "source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type   Singapore strain", "Female Gut Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Gut", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Gut|genetic background:Wild type   Singapore strain", "GSM1376630", "GSM1376630: Female Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376630", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376630", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZG011_CGATGT_L008_R1.fastq.gz", "fastq", 464997192.0, 9117592.0, "GSM1376630 r1", "0:51", "A:94817360;C:107530735;G:141688278;T:120903676;N:57143", 51, null, null, null, 94817360, 107530735, 141688278, 120903676, 57143, "SRX529141", "SRS598838", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00297, null, 0.00033, null, 0.9975, null, 0.62721, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gut", "Digestive System"], [38011, "SRR1265746", "SRX529140", "SRS598837", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Gut Replicate 1 sRNAseq", "GSM1376629", null, "source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type   Singapore strain", "Female Gut Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Gut", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Gut|genetic background:Wild type   Singapore strain", "GSM1376629", "GSM1376629: Female Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376629", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376629", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZG010_ATCACG_L008_R1.fastq.gz", "fastq", 798808308.0, 15662908.0, "GSM1376629 r1", "0:51", "A:163944400;C:183125028;G:240040726;T:211597768;N:100386", 51, null, null, null, 163944400, 183125028, 240040726, 211597768, 100386, "SRX529140", "SRS598837", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.01106, null, 0.00122, null, 0.99466, null, 0.66862, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gut", "Digestive System"], [38012, "SRR1265745", "SRX529139", "SRS598836", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Gut Replicate 3 sRNAseq", "GSM1376628", null, "source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type   Singapore strain", "Male Gut Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Gut", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Gut|genetic background:Wild type   Singapore strain", "GSM1376628", "GSM1376628: Male Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376628", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376628", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZG009_GCCAAT_L007_R1.fastq.gz", "fastq", 224291778.0, 4397878.0, "GSM1376628 r1", "0:51", "A:45043664;C:58692343;G:66840019;T:53695301;N:20451", 51, null, null, null, 45043664, 58692343, 66840019, 53695301, 20451, "SRX529139", "SRS598836", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.0015, null, 0.00021, null, 0.99829, null, 0.69477, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gut", "Digestive System"], [38013, "SRR1265743", "SRX529138", "SRS598835", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Gut Replicate 1 sRNAseq", "GSM1376626", null, "source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type   Singapore strain", "Male Gut Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Gut", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Gut|genetic background:Wild type   Singapore strain", "GSM1376626", "GSM1376626: Male Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376626", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376626", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZG007_TGACCA_L007_R1.fastq.gz", "fastq", 1058961552.0, 20763952.0, "GSM1376626 r1", "0:51", "A:205056709;C:273349362;G:322710601;T:257753257;N:91623", 51, null, null, null, 205056709, 273349362, 322710601, 257753257, 91623, "SRX529138", "SRS598835", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00382, null, 0.00043, null, 0.99746, null, 0.683, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gut", "Digestive System"], [38023, "SRR1265744", "SRX529128", "SRS598826", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Gut Replicate 2 sRNAseq", "GSM1376627", null, "source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type   Singapore strain", "Male Gut Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Gut", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Gut|genetic background:Wild type   Singapore strain", "GSM1376627", "GSM1376627: Male Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376627", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376627", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZG008_ACAGTG_L007_R1.fastq.gz", "fastq", 541064457.0, 10609107.0, "GSM1376627 r1", "0:51", "A:104798947;C:136927266;G:166713427;T:132575036;N:49781", 51, null, null, null, 104798947, 136927266, 166713427, 132575036, 49781, "SRX529128", "SRS598826", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00679, null, 0.00072, null, 0.99655, null, 0.72132, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gut", "Digestive System"], [41072, "SRR3655801", "SRX1836012", "SRS1495476", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "GSM2195935", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195935", "GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq", "GSM2195935", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195935", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS410.fastq.gz", "fastq", 1402184556.0, 18692635.0, "GSM2195935 r1", "0:75.01 1:0", "A:363262740;C:326626075;G:322630446;T:389582075;N:83220", 75, 0, null, null, 363262740, 326626075, 322630446, 389582075, 83220, "SRX1836012", "SRS1495476", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92115, null, 0.08008, null, 0.7389, null, 0.52691, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41073, "SRR3655802", "SRX1836012", "SRS1495476", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "GSM2195935", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195935", "GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq", "GSM2195935", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195935", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS410.fastq.gz", "fastq", 3450884531.0, 46005067.0, "GSM2195935 r2", "0:75.01 1:0", "A:874448337;C:808236306;G:797225707;T:970673048;N:301133", 75, 0, null, null, 874448337, 808236306, 797225707, 970673048, 301133, "SRX1836012", "SRS1495476", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.93035, null, 0.08192, null, 0.73271, null, 0.52273, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41074, "SRR3655799", "SRX1836011", "SRS1495475", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "GSM2195934", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195934", "GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq", "GSM2195934", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195934", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS409.fastq.gz", "fastq", 1422635421.0, 18963577.0, "GSM2195934 r1", "0:75.02 1:0", "A:362173330;C:332883466;G:329078937;T:398420070;N:79618", 75, 0, null, null, 362173330, 332883466, 329078937, 398420070, 79618, "SRX1836011", "SRS1495475", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92474, null, 0.07466, null, 0.73423, null, 0.50871, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41075, "SRR3655800", "SRX1836011", "SRS1495475", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "GSM2195934", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195934", "GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq", "GSM2195934", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195934", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS409.fastq.gz", "fastq", 3549432159.0, 47315580.0, "GSM2195934 r2", "0:75.02 1:0", "A:893492844;C:832741437;G:822208498;T:1000698758;N:290622", 75, 0, null, null, 893492844, 832741437, 822208498, 1000698758, 290622, "SRX1836011", "SRS1495475", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.93197, null, 0.07554, null, 0.73109, null, 0.50825, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41076, "SRR3655797", "SRX1836010", "SRS1495474", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "GSM2195933", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195933", "GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq", "GSM2195933", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195933", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS408.fastq.gz", "fastq", 1400640841.0, 18670640.0, "GSM2195933 r1", "0:75.02 1:0", "A:363544908;C:324586412;G:320620988;T:391797091;N:91442", 75, 0, null, null, 363544908, 324586412, 320620988, 391797091, 91442, "SRX1836010", "SRS1495474", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92971, null, 0.10926, null, 0.73016, null, 0.51418, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41077, "SRR3655798", "SRX1836010", "SRS1495474", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "GSM2195933", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195933", "GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq", "GSM2195933", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195933", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS408.fastq.gz", "fastq", 1400640841.0, 18670640.0, "GSM2195933 r2", "0:75.02 1:0", "A:363544908;C:324586412;G:320620988;T:391797091;N:91442", 75, 0, null, null, 363544908, 324586412, 320620988, 391797091, 91442, "SRX1836010", "SRS1495474", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92977, null, 0.10933, null, 0.73008, null, 0.51355, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41078, "SRR3655795", "SRX1836009", "SRS1495472", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "GSM2195932", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195932", "GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq", "GSM2195932", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195932", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS383.fastq.gz", "fastq", 1510741670.0, 20138480.0, "GSM2195932 r1", "0:75.02 1:0", "A:374411447;C:361418430;G:359803924;T:415021333;N:86536", 75, 0, null, null, 374411447, 361418430, 359803924, 415021333, 86536, "SRX1836009", "SRS1495472", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.94789, null, 0.05269, null, 0.77753, null, 0.53939, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41079, "SRR3655796", "SRX1836009", "SRS1495472", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "GSM2195932", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195932", "GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq", "GSM2195932", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195932", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS383.fastq.gz", "fastq", 3623681121.0, 48303841.0, "GSM2195932 r2", "0:75.02 1:0", "A:881893112;C:869893713;G:867139931;T:1004485159;N:269206", 75, 0, null, null, 881893112, 869893713, 867139931, 1004485159, 269206, "SRX1836009", "SRS1495472", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.95546, null, 0.05225, null, 0.77218, null, 0.53519, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41080, "SRR3655793", "SRX1836008", "SRS1495473", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "GSM2195931", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195931", "GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq", "GSM2195931", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195931", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS381.fastq.gz", "fastq", 1348860046.0, 17985061.0, "GSM2195931 r1", "0:75.00 1:0", "A:350940564;C:313266568;G:309387786;T:375159308;N:105820", 75, 0, null, null, 350940564, 313266568, 309387786, 375159308, 105820, "SRX1836008", "SRS1495473", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92348, null, 0.06356, null, 0.77252, null, 0.52707, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41081, "SRR3655794", "SRX1836008", "SRS1495473", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "GSM2195931", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195931", "GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq", "GSM2195931", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195931", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS381.fastq.gz", "fastq", 3298786881.0, 43979655.0, "GSM2195931 r2", "0:75.01 1:0", "A:829523096;C:775146066;G:763427556;T:930352935;N:337228", 75, 0, null, null, 829523096, 775146066, 763427556, 930352935, 337228, "SRX1836008", "SRS1495473", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.9361, null, 0.06336, null, 0.76353, null, 0.54746, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41082, "SRR3655791", "SRX1836007", "SRS1495471", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "GSM2195930", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195930", "GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq", "GSM2195930", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195930", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS380.fastq.gz", "fastq", 1448364484.0, 19307379.0, "GSM2195930 r1", "0:75.02 1:0", "A:359052072;C:343824905;G:344804667;T:400589883;N:92957", 75, 0, null, null, 359052072, 343824905, 344804667, 400589883, 92957, "SRX1836007", "SRS1495471", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.94277, null, 0.05284, null, 0.77881, null, 0.57769, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41083, "SRR3655792", "SRX1836007", "SRS1495471", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "GSM2195930", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195930", "GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq", "GSM2195930", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195930", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS380.fastq.gz", "fastq", 3599154025.0, 47976708.0, "GSM2195930 r2", "0:75.02 1:0", "A:875615940;C:857379635;G:859609503;T:1006260031;N:288916", 75, 0, null, null, 875615940, 857379635, 859609503, 1006260031, 288916, "SRX1836007", "SRS1495471", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.95037, null, 0.0525, null, 0.77147, null, 0.5711, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41575, "SRR5045902", "SRX2368488", "SRS1814332", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutCV 2", "GSM2401374", null, "source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutCV 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401374", "GSM2401374: MutCV 2; Danio rerio; RNA Seq", "GSM2401374", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401374", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutCV_2.fastq", "fastq", 3876906576.0, 76017776.0, "GSM2401374 r1", "0:51 1:0", "A:957781980;C:915286453;G:859927041;T:1143804372;N:106730", 51, 0, null, null, 957781980, 915286453, 859927041, 1143804372, 106730, "SRX2368488", "SRS1814332", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96196, null, 0.11375, null, 0.70887, null, 0.53406, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41576, "SRR5045901", "SRX2368487", "SRS1814330", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutCV 1", "GSM2401373", null, "source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutCV 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401373", "GSM2401373: MutCV 1; Danio rerio; RNA Seq", "GSM2401373", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401373", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutCV_1.fastq", "fastq", 3835824444.0, 75212244.0, "GSM2401373 r1", "0:51 1:0", "A:946407906;C:904393791;G:851683286;T:1133241327;N:98134", 51, 0, null, null, 946407906, 904393791, 851683286, 1133241327, 98134, "SRX2368487", "SRS1814330", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.95795, null, 0.11761, null, 0.70481, null, 0.53357, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41577, "SRR5045900", "SRX2368486", "SRS1814331", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutGF 2", "GSM2401372", null, "source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutGF 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401372", "GSM2401372: MutGF 2; Danio rerio; RNA Seq", "GSM2401372", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401372", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutGF_2.fastq", "fastq", 3299677866.0, 64699566.0, "GSM2401372 r1", "0:51 1:0", "A:809247440;C:784035543;G:731742820;T:974610541;N:41522", 51, 0, null, null, 809247440, 784035543, 731742820, 974610541, 41522, "SRX2368486", "SRS1814331", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96247, null, 0.1049, null, 0.74034, null, 0.5525, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41578, "SRR5045899", "SRX2368485", "SRS1814329", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutGF 1", "GSM2401371", null, "source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutGF 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401371", "GSM2401371: MutGF 1; Danio rerio; RNA Seq", "GSM2401371", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401371", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutGF_1.fastq", "fastq", 3734921199.0, 73233749.0, "GSM2401371 r1", "0:51 1:0", "A:923493830;C:879193170;G:840678282;T:1091454504;N:101413", 51, 0, null, null, 923493830, 879193170, 840678282, 1091454504, 101413, "SRX2368485", "SRS1814329", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96328, null, 0.1099, null, 0.73492, null, 0.50455, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41579, "SRR5045898", "SRX2368484", "SRS1814328", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTCV 3", "GSM2401370", null, "source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTCV 3", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401370", "GSM2401370: WTCV 3; Danio rerio; RNA Seq", "GSM2401370", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401370", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTCV_3.fastq", "fastq", 3928418412.0, 77027812.0, "GSM2401370 r1", "0:51 1:0", "A:966197912;C:939595492;G:912123411;T:1110393846;N:107751", 51, 0, null, null, 966197912, 939595492, 912123411, 1110393846, 107751, "SRX2368484", "SRS1814328", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97188, null, 0.08862, null, 0.7357, null, 0.53339, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41580, "SRR5045897", "SRX2368483", "SRS1814327", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTCV 2", "GSM2401369", null, "source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTCV 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401369", "GSM2401369: WTCV 2; Danio rerio; RNA Seq", "GSM2401369", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401369", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTCV_2.fastq", "fastq", 3782941473.0, 74175323.0, "GSM2401369 r1", "0:51 1:0", "A:928563733;C:910471684;G:872137892;T:1071716851;N:51313", 51, 0, null, null, 928563733, 910471684, 872137892, 1071716851, 51313, "SRX2368483", "SRS1814327", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97097, null, 0.09668, null, 0.74255, null, 0.55455, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41581, "SRR5045896", "SRX2368482", "SRS1814326", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTCV 1", "GSM2401368", null, "source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTCV 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401368", "GSM2401368: WTCV 1; Danio rerio; RNA Seq", "GSM2401368", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401368", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTCV_1.fastq", "fastq", 3643146954.0, 71434254.0, "GSM2401368 r1", "0:51 1:0", "A:877377891;C:875020597;G:839793450;T:1050862579;N:92437", 51, 0, null, null, 877377891, 875020597, 839793450, 1050862579, 92437, "SRX2368482", "SRS1814326", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.9683, null, 0.08514, null, 0.73525, null, 0.55486, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41582, "SRR5045895", "SRX2368481", "SRS1814325", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTGF 3", "GSM2401367", null, "source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTGF 3", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401367", "GSM2401367: WTGF 3; Danio rerio; RNA Seq", "GSM2401367", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401367", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTGF_3.fastq", "fastq", 3462802386.0, 67898086.0, "GSM2401367 r1", "0:51 1:0", "A:843407439;C:830117704;G:803633976;T:985548502;N:94765", 51, 0, null, null, 843407439, 830117704, 803633976, 985548502, 94765, "SRX2368481", "SRS1814325", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97202, null, 0.08623, null, 0.75939, null, 0.56558, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41583, "SRR5045894", "SRX2368480", "SRS1814324", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTGF 2", "GSM2401366", null, "source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTGF 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401366", "GSM2401366: WTGF 2; Danio rerio; RNA Seq", "GSM2401366", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401366", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTGF_2.fastq", "fastq", 3699149799.0, 72532349.0, "GSM2401366 r1", "0:51 1:0", "A:907425678;C:884609705;G:855651232;T:1051368070;N:95114", 51, 0, null, null, 907425678, 884609705, 855651232, 1051368070, 95114, "SRX2368480", "SRS1814324", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96861, null, 0.08856, null, 0.75223, null, 0.55327, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41584, "SRR5045893", "SRX2368479", "SRS1814323", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTGF 1", "GSM2401365", null, "source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTGF 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401365", "GSM2401365: WTGF 1; Danio rerio; RNA Seq", "GSM2401365", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401365", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTGF_1.fastq", "fastq", 3948593247.0, 77423397.0, "GSM2401365 r1", "0:51 1:0", "A:951060123;C:949871425;G:909862458;T:1137745436;N:53805", 51, 0, null, null, 951060123, 949871425, 909862458, 1137745436, 53805, "SRX2368479", "SRS1814323", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97252, null, 0.08483, null, 0.74418, null, 0.54605, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [44999, "SRR6411468", "SRX3504483", "SRS2782037", "SRP127389", "PRJNA427282", "RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]", "GSE108436", "Transcriptome Analysis", "Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a \u201cmiRNA matrix\u201d that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues  gut and liver under homesostasis.", "parent bioproject:PRJNA427275", "pubmed:30386173", null, "Gut 4 miRNA", "GSM2898188", null, "source name:Gut|tissue:Gut|Sex:male", "Gut 4 miRNA", "Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp\u2019s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output. Gut 1  Gut 2  Liver 1 and Liver 2  contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.", "Gut", "Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26\u201329 \u00b0C  and the light\u2013dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at \u201370 \u00b0C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA", null, "tissue:Gut|Sex:male", "GSM2898188", "GSM2898188: Gut 4 miRNA; Danio rerio; miRNA Seq", "GSM2898188", null, "1", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA", "GEO Accession:GSM2898188", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP127389", null, null, "4.fastq.gz", "fastq", 643103727.0, 12609877.0, "GSM2898188 r1", "0:51", "A:158299708;C:154230134;G:180978224;T:147874496;N:1721165", 51, null, null, null, 158299708, 154230134, 180978224, 147874496, 1721165, "SRX3504483", "SRS2782037", "SRA641250", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", 1, 0.0075, null, 0.00106, null, 0.99671, null, 0.56044, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-12-22", "Undetermined", "Adult", "Gut", "Digestive System"], [45000, "SRR6411467", "SRX3504482", "SRS2782036", "SRP127389", "PRJNA427282", "RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]", "GSE108436", "Transcriptome Analysis", "Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a \u201cmiRNA matrix\u201d that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues  gut and liver under homesostasis.", "parent bioproject:PRJNA427275", "pubmed:30386173", null, "Gut 3 miRNA", "GSM2898187", null, "source name:Gut|tissue:Gut|Sex:male", "Gut 3 miRNA", "Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp\u2019s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing  alignment  mature/precursor/ novel miRNA detection and quantification  and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data  and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output. Gut 1  Gut 2  Liver 1 and Liver 2  contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol  GeneID  Description and MirBaseID represent miRNA annotation and description information.", "Gut", "Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26\u201329 \u00b0C  and the light\u2013dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at \u201370 \u00b0C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA", null, "tissue:Gut|Sex:male", "GSM2898187", "GSM2898187: Gut 3 miRNA; Danio rerio; miRNA Seq", "GSM2898187", null, "1", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA", "GEO Accession:GSM2898187", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP127389", null, null, "3.fastq.gz", "fastq", 657326148.0, 12888748.0, "GSM2898187 r1", "0:51", "A:155617794;C:161709285;G:186002579;T:152250836;N:1745654", 51, null, null, null, 155617794, 161709285, 186002579, 152250836, 1745654, "SRX3504482", "SRS2782036", "SRA641250", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", 1, 0.11293, null, 0.00924, null, 0.99399, null, 0.58458, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-12-22", "Undetermined", "Adult", "Gut", "Digestive System"], [45003, "SRR6411472", "SRX3504487", "SRS2782041", "SRP127390", "PRJNA427283", "RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA]", "GSE108435", "Transcriptome Analysis", "Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a \u201cmiRNA matrix\u201d that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues  liver and gut.", "parent bioproject:PRJNA427275", "pubmed:30386173", null, "Gut 4 mRNA", "GSM2898184", null, "source name:Gut|Sex:male|tissue:Gut", "Gut 4 mRNA", "Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp\u2019s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison.  Columns to the right of the Base Mean column represent standard DEseq2 output.  Gut 1  Gut 2  Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id  external gene name  description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers  hsapiens homolog ensembl gene  hgnc symbol  Human description and Human entrez geneid", "Gut", "Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26\u201329 \u00b0C  and the light\u2013dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at \u201370 \u00b0C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.", null, "Sex:male|tissue:Gut", "GSM2898184", "GSM2898184: Gut 4 mRNA; Danio rerio; RNA Seq", "GSM2898184", null, "1", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.", "GEO Accession:GSM2898184", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP127390", null, null, "Gut_2.fastq.gz", "fastq", 2511580170.0, 49246670.0, "GSM2898184 r1", "0:51", "A:634532680;C:591744395;G:630819200;T:654046479;N:437416", 51, null, null, null, 634532680, 591744395, 630819200, 654046479, 437416, "SRX3504487", "SRS2782041", "SRA641251", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", 1, 0.91491, null, 0.06302, null, 0.79632, null, 0.54435, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-12-22", "Undetermined", "Undetermined", "Gut", "Digestive System"], [45004, "SRR6411471", "SRX3504486", "SRS2782040", "SRP127390", "PRJNA427283", "RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA]", "GSE108435", "Transcriptome Analysis", "Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a \u201cmiRNA matrix\u201d that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues  liver and gut.", "parent bioproject:PRJNA427275", "pubmed:30386173", null, "Gut 3 mRNA", "GSM2898183", null, "source name:Gut|Sex:male|tissue:Gut", "Gut 3 mRNA", "Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp\u2019s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison.  Columns to the right of the Base Mean column represent standard DEseq2 output.  Gut 1  Gut 2  Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id  external gene name  description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers  hsapiens homolog ensembl gene  hgnc symbol  Human description and Human entrez geneid", "Gut", "Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26\u201329 \u00b0C  and the light\u2013dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at \u201370 \u00b0C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.", null, "Sex:male|tissue:Gut", "GSM2898183", "GSM2898183: Gut 3 mRNA; Danio rerio; RNA Seq", "GSM2898183", null, "1", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.", "GEO Accession:GSM2898183", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP127390", null, null, "Gut_1.fastq.gz", "fastq", 2336820153.0, 45820003.0, "GSM2898183 r1", "0:51", "A:592745033;C:551283776;G:583859269;T:608544280;N:387795", 51, null, null, null, 592745033, 551283776, 583859269, 608544280, 387795, "SRX3504486", "SRS2782040", "SRA641251", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-12-22", "Undetermined", "Undetermined", "Gut", "Digestive System"], [53019, "SRR9662020", "SRX6422896", "SRS5079686", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA Seq Intestine rep2", "GSM3934888", null, "source name:Tissue|strain:Tuebingen|tissue:Intestine", "YueLab RNA Seq Intestine rep2", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "Tissue", null, "For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly  polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Intestine", "GSM3934888", "GSM3934888: YueLab RNA Seq Intestine rep2; Danio rerio; RNA Seq", "GSM3934888", null, "1", "For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "GEO Accession:GSM3934888", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Intestine-rep2_SE.fastq.gz", "fastq", 1692722829.0, 30387989.0, "GSM3934888 r1", "0:55.70", "A:384930576;C:443068642;G:407616609;T:444110335;N:12996667", 55, null, null, null, 384930576, 443068642, 407616609, 444110335, 12996667, "SRX6422896", "SRS5079686", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 1, 0.9407, null, 0.20429, null, 0.80071, null, 0.63627, null, 51, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Gut", "Digestive System"], [55495, "SRR10511896", "SRX7200010", "SRS5705565", "SRP231178", "PRJNA591019", "Gene expression in the adult zebrafish intestine during starvation and refeeding", "GSE140821", "Transcriptome Analysis", "In this RNA Seq dataset  we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes  including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf  dpf that were separately housed. One treatment group control was continuously fed throughout the study  while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding  4 zebrafish were taken from each treatment group  euthanized  and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.", null, "pubmed:35317738", null, "3dpRSta2Gut2", "GSM4187022", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 409993093, 286631833, 275766237, 425009393, 52994, "SRX7200010", "SRS5705565", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.9238, null, 0.127, null, 0.74718, null, 0.55171, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpRSta2Gut1", "GSM4187021", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 451585039, 329412420, 316009619, 474302622, 59511, "SRX7200009", "SRS5705564", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.92047, null, 0.12142, null, 0.74785, null, 0.56011, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpRSta1Gut3", "GSM4187020", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 422349451, 308266246, 300748378, 442499660, 54982, "SRX7200008", "SRS5705563", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93232, null, 0.10841, null, 0.7573, null, 0.53817, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpRSta1Gut1", "GSM4187019", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 451110725, 322314892, 308247205, 469898838, 58613, "SRX7200007", "SRS5705562", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.9272, null, 0.11972, null, 0.75822, null, 0.54861, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpRFed2Gut3", "GSM4187018", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 406259184, 299540462, 297537630, 425792267, 54014, "SRX7200006", "SRS5705561", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93776, null, 0.10446, null, 0.75659, null, 0.51357, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpRFed2Gut2", "GSM4187017", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 499095968, 376678270, 363861124, 526664286, 66227, "SRX7200005", "SRS5705560", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93356, null, 0.10506, null, 0.75812, null, 0.54405, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpSFed1Gut3", "GSM4187008", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 429617322, 351337972, 347154272, 464366202, 57066, "SRX7200004", "SRS5705559", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93898, null, 0.09149, null, 0.75568, null, 0.51578, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpSFed1Gut1", "GSM4187007", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 441324595, 335749891, 331699440, 466684268, 56501, "SRX7200003", "SRS5705558", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93304, null, 0.11059, null, 0.75286, null, 0.55511, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpSSta2Gut3", "GSM4187006", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 509554159, 377147211, 365503374, 533656366, 56839, "SRX7200002", "SRS5705557", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93641, null, 0.11479, null, 0.75351, null, 0.53275, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpSSta2Gut2", "GSM4187005", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 495592326, 391304311, 373137484, 529784276, 55928, "SRX7200001", "SRS5705556", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.9421, null, 0.1111, null, 0.74566, null, 0.54158, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpSSta1Gut2", "GSM4187004", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 483646499, 336487643, 323951194, 497225233, 52011, "SRX7200000", "SRS5705555", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.9344, null, 0.13244, null, 0.74734, null, 0.52964, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpSSta1Gut1", "GSM4187003", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 454772545, 325458319, 321434801, 469947006, 50861, "SRX7199999", "SRS5705554", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93659, null, 0.11683, null, 0.75213, null, 0.52836, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpSFed2Gut3", "GSM4187002", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 467439399, 310187678, 304525609, 479032805, 50683, "SRX7199998", "SRS5705553", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93358, null, 0.14283, null, 0.74939, null, 0.56013, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpSFed2Gut2", "GSM4187001", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 567770670, 395455630, 379200223, 585057600, 61132, "SRX7199997", "SRS5705552", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93207, null, 0.13563, null, 0.75144, null, 0.54701, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpRFed1Gut3", "GSM4187016", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 478883149, 377608593, 368322683, 508321013, 64729, "SRX7199996", "SRS5705551", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93695, null, 0.09593, null, 0.75341, null, 0.55416, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpRFed1Gut2", "GSM4187015", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 472266921, 343820482, 331431433, 491557290, 63364, "SRX7199995", "SRS5705550", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.92641, null, 0.11798, null, 0.74614, null, 0.55037, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpSSta2Gut3", "GSM4187014", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 568790177, 410992982, 388696297, 588697675, 71034, "SRX7199994", "SRS5705549", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.937, null, 0.12586, null, 0.75921, null, 0.53627, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpSSta2Gut2", "GSM4187013", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 483227292, 368630214, 361368304, 509108986, 62704, "SRX7199993", "SRS5705548", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.94065, null, 0.11314, null, 0.73726, null, 0.53094, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpsSta2Gut1", "GSM4187012", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 535885753, 401729105, 382301792, 563061958, 68025, "SRX7199992", "SRS5705547", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.94161, null, 0.11585, null, 0.74848, null, 0.50594, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpSSta1Gut2", "GSM4187011", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 515524495, 386623119, 369300060, 538958945, 65331, "SRX7199991", "SRS5705546", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93788, null, 0.1201, null, 0.73576, null, 0.536, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpSFed2Gut3", "GSM4187010", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 456360065, 335880726, 319279080, 483257577, 58087, "SRX7199990", "SRS5705545", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.935, null, 0.11846, null, 0.7556, null, 0.54994, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "21dpsFed2Gut1", "GSM4187009", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 467924183, 353835126, 340667908, 495293545, 59279, "SRX7199989", "SRS5705544", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.93452, null, 0.1059, null, 0.75897, null, 0.56316, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35317738", null, "3dpSFed1Gut1", "GSM4187000", null, "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", null, "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\u2019s 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", null, "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", null, "SRP231178", null, null, "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, null, null, 438395339, 340541415, 338487129, 462497338, 49752, "SRX7199988", "SRS5705543", "SRA1000332", "GEO", "Molecular Genetics and Microbiology, Duke University", 1, 0.94225, null, 0.09616, null, 0.76021, null, 0.53717, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2019-11-21", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [60007, "SRR12109607", "SRX8633610", "SRS6920345", "SRP269241", "PRJNA641989", "Zebrafish intestinal SmallRNA", "PRJNA641989", "Other", "A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.", null, null, null, null, "Drt3", null, "strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish intestine", "F", "F", "BGISEQ", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP269241", null, "loader:fastq load.py", "Drt3.fq.gz", "fastq", 953116651.0, 39450392.0, "Drt3.fq.gz", "0:24.16", "A:165275545;C:266933722;G:285524079;T:235383107;N:198", 24, null, null, null, 165275545, 266933722, 285524079, 235383107, 198, "SRX8633610", "SRS6920345", "SRA1092425", "Kunming University of Science and Technology|faculty of life science and technology", "Kunming University of Science and Technology", 1, 0.86243, null, 0.21541, null, 0.80294, null, 0.67181, null, 29, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-10", "Adult", "Adult", "Gut", "Digestive System"], [60008, "SRR12109608", "SRX8633609", "SRS6920344", "SRP269241", "PRJNA641989", "Zebrafish intestinal SmallRNA", "PRJNA641989", "Other", "A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.", null, null, null, null, "Drt2", null, "strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish intestine", "E", "E", "BGISEQ", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP269241", null, "loader:fastq load.py", "Drt2.fq.gz", "fastq", 629335361.0, 26037543.0, "Drt2.fq.gz", "0:24.17", "A:111827613;C:172564695;G:192159133;T:152783892;N:28", 24, null, null, null, 111827613, 172564695, 192159133, 152783892, 28, "SRX8633609", "SRS6920344", "SRA1092425", "Kunming University of Science and Technology|faculty of life science and technology", "Kunming University of Science and Technology", 1, 0.86328, null, 0.21943, null, 0.7992, null, 0.64786, null, 26, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-10", "Adult", "Adult", "Gut", "Digestive System"], [60009, "SRR12109609", "SRX8633608", "SRS6920343", "SRP269241", "PRJNA641989", "Zebrafish intestinal SmallRNA", "PRJNA641989", "Other", "A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.", null, null, null, null, "Drt1", null, "strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish intestine", "D", "D", "BGISEQ", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP269241", null, "loader:fastq load.py", "Drt1.fq.gz", "fastq", 898185854.0, 37273958.0, "Drt1.fq.gz", "0:24.10", "A:155257170;C:247725871;G:276963807;T:218238980;N:26", 24, null, null, null, 155257170, 247725871, 276963807, 218238980, 26, "SRX8633608", "SRS6920343", "SRA1092425", "Kunming University of Science and Technology|faculty of life science and technology", "Kunming University of Science and Technology", 1, 0.86686, null, 0.21764, null, 0.79508, null, 0.6694, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-10", "Adult", "Adult", "Gut", "Digestive System"], [60010, "SRR12109610", "SRX8633607", "SRS6920342", "SRP269241", "PRJNA641989", "Zebrafish intestinal SmallRNA", "PRJNA641989", "Other", "A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.", null, null, null, null, "Drc3", null, "strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish intestine", "C", "C", "BGISEQ", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP269241", null, "loader:fastq load.py", "Drc3.fq.gz", "fastq", 912782161.0, 35931507.0, "Drc3.fq.gz", "0:25.40", "A:153448479;C:252628189;G:280829895;T:225874586;N:1012", 25, null, null, null, 153448479, 252628189, 280829895, 225874586, 1012, "SRX8633607", "SRS6920342", "SRA1092425", "Kunming University of Science and Technology|faculty of life science and technology", "Kunming University of Science and Technology", 1, 0.89797, null, 0.21308, null, 0.80823, null, 0.62611, null, 23, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-10", "Adult", "Adult", "Gut", "Digestive System"], [60011, "SRR12109611", "SRX8633606", "SRS6920341", "SRP269241", "PRJNA641989", "Zebrafish intestinal SmallRNA", "PRJNA641989", "Other", "A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.", null, null, null, null, "Drc2", null, "strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish intestine", "B", "B", "BGISEQ", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP269241", null, "loader:fastq load.py", "Drc2.fq.gz", "fastq", 784553020.0, 31429473.0, "Drc2.fq.gz", "0:24.96", "A:128271350;C:223302609;G:241310233;T:191668193;N:635", 24, null, null, null, 128271350, 223302609, 241310233, 191668193, 635, "SRX8633606", "SRS6920341", "SRA1092425", "Kunming University of Science and Technology|faculty of life science and technology", "Kunming University of Science and Technology", 1, 0.9087, null, 0.20487, null, 0.80805, null, 0.67324, null, 30, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-10", "Adult", "Adult", "Gut", "Digestive System"], [60012, "SRR12109612", "SRX8633605", "SRS6920340", "SRP269241", "PRJNA641989", "Zebrafish intestinal SmallRNA", "PRJNA641989", "Other", "A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.", null, null, null, null, "Drc1", null, "strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish intestine", "A", "A", "BGISEQ", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP269241", null, "loader:fastq load.py", "Drc1.fq.gz", "fastq", 814894343.0, 32234530.0, "Drc1.fq.gz", "0:25.28", "A:133616147;C:230834630;G:253965304;T:196477437;N:825", 25, null, null, null, 133616147, 230834630, 253965304, 196477437, 825, "SRX8633605", "SRS6920340", "SRA1092425", "Kunming University of Science and Technology|faculty of life science and technology", "Kunming University of Science and Technology", 1, 0.89344, null, 0.21273, null, 0.80738, null, 0.66815, null, 28, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-10", "Adult", "Adult", "Gut", "Digestive System"], [62742, "SRR13360748", "SRX9785053", "SRS7972286", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "macrogard", "macrogard2", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "PM2", "PM2", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "pm2_S8_R1_001.fastq.gz", "fastq", 3517898944.0, 46288144.0, "pm2 S8 R1 001.fastq.gz", "0:76 1:0", "A:914616261;C:828363626;G:805674434;T:969167482;N:77141", 76, 0, null, null, 914616261, 828363626, 805674434, 969167482, 77141, "SRX9785053", "SRS7972286", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.94008, null, 0.0747, null, 0.71394, null, 0.51572, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62743, "SRR13360749", "SRX9785052", "SRS7972285", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "macrogard", "macrogard1", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "PM1", "PM1", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "pm1_S7_R1_001.fastq.gz", "fastq", 1974822380.0, 25984505.0, "pm1 S7 R1 001.fastq.gz", "0:76 1:0", "A:561606319;C:416363486;G:408486827;T:588324386;N:41362", 76, 0, null, null, 561606319, 416363486, 408486827, 588324386, 41362, "SRX9785052", "SRS7972285", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.9274, null, 0.16109, null, 0.74351, null, 0.57108, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62744, "SRR13360750", "SRX9785051", "SRS7972284", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "soybean", "soybean4", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CP4", "CP4", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cp4_S4_R1_001.fastq.gz", "fastq", 2913402316.0, 38334241.0, "cp4 S4 R1 001.fastq.gz", "0:76 1:0", "A:791131658;C:648321809;G:621173454;T:852725371;N:50024", 76, 0, null, null, 791131658, 648321809, 621173454, 852725371, 50024, "SRX9785051", "SRS7972284", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.93191, null, 0.1275, null, 0.7333, null, 0.55298, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62745, "SRR13360751", "SRX9785050", "SRS7972283", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "soybean", "soybean3", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CP3", "CP3", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cp3_S6_R1_001.fastq.gz", "fastq", 2648220684.0, 34845009.0, "cp3 S6 R1 001.fastq.gz", "0:76 1:0", "A:697194378;C:597685138;G:585283565;T:767999519;N:58084", 76, 0, null, null, 697194378, 597685138, 585283565, 767999519, 58084, "SRX9785050", "SRS7972283", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.93629, null, 0.1048, null, 0.7349, null, 0.54364, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62746, "SRR13360752", "SRX9785049", "SRS7972282", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "soybean", "soybean2", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CP2", "CP2", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cp2_S5_R1_001.fastq.gz", "fastq", 2339410872.0, 30781722.0, "cp2 S5 R1 001.fastq.gz", "0:76 1:0", "A:620056592;C:539298564;G:520500416;T:659503250;N:52050", 76, 0, null, null, 620056592, 539298564, 520500416, 659503250, 52050, "SRX9785049", "SRS7972282", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.93909, null, 0.0916, null, 0.70942, null, 0.51709, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62747, "SRR13360753", "SRX9785048", "SRS7972281", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "soybean", "soybean1", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CP1", "CP1", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cp1_S4_R1_001.fastq.gz", "fastq", 2271445592.0, 29887442.0, "cp1 S4 R1 001.fastq.gz", "0:76 1:0", "A:620595380;C:508382666;G:499686333;T:642731924;N:49289", 76, 0, null, null, 620595380, 508382666, 499686333, 642731924, 49289, "SRX9785048", "SRS7972281", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.93497, null, 0.1129, null, 0.71127, null, 0.50787, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62748, "SRR13360754", "SRX9785047", "SRS7972280", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "control", "control4", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CZ4", "CZ4", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cz4_S1_R1_001.fastq.gz", "fastq", 2772612848.0, 36481748.0, "cz4 S1 R1 001.fastq.gz", "0:76 1:0", "A:753409223;C:625962831;G:590503241;T:802690640;N:46913", 76, 0, null, null, 753409223, 625962831, 590503241, 802690640, 46913, "SRX9785047", "SRS7972280", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.92942, null, 0.15362, null, 0.62889, null, 0.51867, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62749, "SRR13360755", "SRX9785046", "SRS7972279", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "control", "control3", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CZ3", "CZ3", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cz3_S3_R1_001.fastq.gz", "fastq", 2424287672.0, 31898522.0, "cz3 S3 R1 001.fastq.gz", "0:76 1:0", "A:629966430;C:571438897;G:558947157;T:663881953;N:53235", 76, 0, null, null, 629966430, 571438897, 558947157, 663881953, 53235, "SRX9785046", "SRS7972279", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.94199, null, 0.04836, null, 0.72218, null, 0.48478, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62750, "SRR13360756", "SRX9785045", "SRS7972278", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "macrogard", "macrogard4", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "PM4", "PM4", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "pm4_S7_R1_001.fastq.gz", "fastq", 2901513560.0, 38177810.0, "pm4 S7 R1 001.fastq.gz", "0:76 1:0", "A:737189471;C:698799076;G:664901115;T:800575145;N:48753", 76, 0, null, null, 737189471, 698799076, 664901115, 800575145, 48753, "SRX9785045", "SRS7972278", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.95173, null, 0.04367, null, 0.74089, null, 0.50116, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62751, "SRR13360757", "SRX9785044", "SRS7972277", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "macrogard", "macrogard3", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "PM3", "PM3", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "pm3_S9_R1_001.fastq.gz", "fastq", 3148390744.0, 41426194.0, "pm3 S9 R1 001.fastq.gz", "0:76 1:0", "A:834545372;C:725073648;G:704241250;T:884462724;N:67750", 76, 0, null, null, 834545372, 725073648, 704241250, 884462724, 67750, "SRX9785044", "SRS7972277", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.94256, null, 0.09248, null, 0.72099, null, 0.52303, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62752, "SRR13360758", "SRX9785043", "SRS7972276", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "control", "control2", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CZ2", "CZ2", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cz2_S2_R1_001.fastq", "fastq", 2207708116.0, 29048791.0, "cz2 S2 R1 001.fastq", "0:76 1:0", "A:614048827;C:488071931;G:474165427;T:631372646;N:49285", 76, 0, null, null, 614048827, 488071931, 474165427, 631372646, 49285, "SRX9785043", "SRS7972276", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.93271, null, 0.12538, null, 0.71733, null, 0.53166, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62753, "SRR13360759", "SRX9785042", "SRS7972275", "SRP300470", "PRJNA689790", "Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish", "PRJNA689790", "Other", "We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.", null, null, null, "control", "control1", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "CZ1", "CZ1", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP300470", null, null, "cz1_S1_R1_001.fastq.gz", "fastq", 2264115696.0, 29790996.0, "cz1 S1 R1 001.fastq.gz", "0:76 1:0", "A:619936364;C:496981021;G:501038961;T:646109550;N:49800", 76, 0, null, null, 619936364, 496981021, 501038961, 646109550, 49800, "SRX9785042", "SRS7972275", "SRA1180489", "Nord University|Faculty of Bioscience", "Nord University", 1, 0.93737, null, 0.1307, null, 0.73003, null, 0.55416, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2021-01-05", "Juvenile", "Juvenile", "Gut", "Digestive System"], [62981, "SRR13559185", "SRX9957470", "SRS8131854", "SRP303451", "PRJNA695140", "Zebrafish caloric restriction", "PRJNA695140", "Other", "Using Zebrafish Danio rerio as a model organism for aquaculture  we investigated the impact of caloric restriction CR on growth  gut morphology and gene expression.", null, null, null, "100% feeding group replicate 2", "CR 100perc 2", null, "strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:100% feeding|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 100% feeding", "CR 100perc 2", "CR 100perc 2", "Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. 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"nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63079, "SRR13593805", "SRX9988311", "SRS8159458", "SRP304042", "PRJNA698416", "Inhibition of goblet cell differentiation in hypothyroidism is associated with deregulated Fgf19 Fgfr4 signaling", "PRJNA698416", "Other", "To understand the effect of thyroid hormone", null, null, null, "Control sample rep 2", "CS2", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:adult|dev stage:not applicable|sex:male|tissue:Gut 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerion gut RNA seq", "Control sample rep 2", "Control sample rep 2", "RNA sequencing for danio rerion gut", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP304042", null, null, "Einat_control_gut_2_R1.fastq", "fastq", 1541134836.0, 20684259.0, "Einat control gut 2 R1.fastq", "0:74.51 1:0", "A:387937126;C:363944491;G:348612093;T:440600639;N:40487", 74, 0, null, null, 387937126, 363944491, 348612093, 440600639, 40487, "SRX9988311", "SRS8159458", "SRA1189900", "Bar Ilan University|life science", "Bar Ilan University", 1, 0.94793, null, 0.0608, null, 0.80476, null, 0.52377, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63080, "SRR13593806", "SRX9988310", "SRS8159456", "SRP304042", "PRJNA698416", "Inhibition of goblet cell differentiation in hypothyroidism is associated with deregulated Fgf19 Fgfr4 signaling", "PRJNA698416", "Other", "To understand the effect of thyroid hormone", null, null, null, "Control sample rep 1", "CS1", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:adult|dev stage:not applicable|sex:male|tissue:Gut 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerion gut RNA seq", "Control sample rep 1", "Control sample rep 1", "RNA sequencing for danio rerion gut", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP304042", null, null, "Einat_control_gut_1_R1.fastq", "fastq", 1538665984.0, 20648801.0, "Einat control gut 1 R1.fastq", "0:74.52 1:0", "A:381368703;C:366635633;G:353200844;T:437407142;N:53662", 74, 0, null, null, 381368703, 366635633, 353200844, 437407142, 53662, "SRX9988310", "SRS8159456", "SRA1189900", "Bar Ilan University|life science", "Bar Ilan University", 1, 0.9476, null, 0.05307, null, 0.81134, null, 0.54676, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63810, "SRR14060980", "SRX10435564", "SRS8569035", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor+radiation [18 24 M2 RAD]", "GSM5208645", null, "tissue:Gastrointestinal tract", "Torpor+radiation [18 24 M2 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output", "Gastrointestinal tract", "A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208645", "GSM5208645: Torpor+radiation [18 24 M2 RAD]; Danio rerio; RNA Seq", "GSM5208645", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208645", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "18-24-M2-RAD_GTGAAA_S103_L008_R1_001.fastq.gz", "fastq", 1589596300.0, 31791926.0, "GSM5208645 r1", "0:50", "A:343218732;C:412078303;G:480421414;T:353581599;N:296252", 50, null, null, null, 343218732, 412078303, 480421414, 353581599, 296252, "SRX10435564", "SRS8569035", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.61709, null, 0.13219, null, 0.8379, null, 0.67633, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63811, "SRR14060979", "SRX10435563", "SRS8569036", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor+radiation [18 24 M1 RAD]", "GSM5208644", null, "tissue:Gastrointestinal tract", "Torpor+radiation [18 24 M1 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output", "Gastrointestinal tract", "A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208644", "GSM5208644: Torpor+radiation [18 24 M1 RAD]; Danio rerio; RNA Seq", "GSM5208644", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208644", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "18-24-M1-RAD_GTCCGC_S102_L008_R1_001.fastq.gz", "fastq", 1826597250.0, 36531945.0, "GSM5208644 r1", "0:50", "A:400114581;C:473398494;G:532511254;T:420225243;N:347678", 50, null, null, null, 400114581, 473398494, 532511254, 420225243, 347678, "SRX10435563", "SRS8569036", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.58111, null, 0.13543, null, 0.86419, null, 0.68781, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"]], "truncated": 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