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null, null, null, null, "Zebrafish intestine", null, "strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Intestinal Transcriptome", "K 1 1.fq", "K 1 1.fq", "Intestinal Transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP454395", null, null, "K-1_1.fq.gz K-1_2.fq.gz", "fastq fastq", 7164142200.0, 23880474.0, "K 1 1.fq.gz", "0:150 1:150", "A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789", 150, 150, null, null, 1896647470, 1661542391, 1700422400, 1905500150, 29789, "SRX21322821", "SRS18569855", "SRA1689922", "Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish", "Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences", 2, 0.94635, 0.94209, 0.03738, 0.03664, 0.71961, 0.72571, 0.45014, 0.44857, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-10", "Undetermined", "Undetermined", "Gut", "Digestive System"], [29041, "SRR26990794", "SRX22683825", "SRS19677539", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "WT gut3", "GSM7924158", null, "source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT gut3", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "gut", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:wildtype|time:50dpf", "GSM7924158", "GSM7924158: WT gut3; Danio rerio; RNA Seq", "GSM7924158 r1", "GSM7924158", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz", "fastq fastq", 6066709786.0, 20088443.0, "GSM7924158 r1", "0:151 1:151", "A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156", 151, 151, null, null, 1673762656, 1360901090, 1385125931, 1646863953, 56156, "SRX22683825", "SRS19677539", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.92515, 0.9297, 0.0691, 0.0659, 0.75041, 0.75022, 0.53007, 0.53064, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29042, "SRR26990795", "SRX22683824", "SRS19677538", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "WT gut2", "GSM7924157", null, "source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT gut2", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "gut", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:wildtype|time:50dpf", "GSM7924157", "GSM7924157: WT gut2; Danio rerio; RNA Seq", "GSM7924157 r1", "GSM7924157", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz", "fastq fastq", 5406867570.0, 17903535.0, "GSM7924157 r1", "0:151 1:151", "A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612", 151, 151, null, null, 1464846243, 1237183908, 1259215309, 1445572498, 49612, "SRX22683824", "SRS19677538", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93795, 0.94322, 0.05952, 0.05592, 0.75933, 0.75887, 0.54179, 0.53451, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29043, "SRR26990796", "SRX22683823", "SRS19677537", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "WT gut1", "GSM7924156", null, "source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT gut1", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "gut", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:wildtype|time:50dpf", "GSM7924156", "GSM7924156: WT gut1; Danio rerio; RNA Seq", "GSM7924156 r1", "GSM7924156", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz", "fastq fastq", 5162192908.0, 17093354.0, "GSM7924156 r1", "0:151 1:151", "A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343", 151, 151, null, null, 1404682153, 1175657030, 1196829496, 1384975886, 48343, "SRX22683823", "SRS19677537", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93119, 0.93585, 0.06122, 0.05809, 0.74757, 0.74757, 0.54124, 0.54417, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29044, "SRR26990797", "SRX22683822", "SRS19677536", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "itgavKO gut3", "GSM7924155", null, "source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO gut3", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "gut", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:itgavKO mutant|time:50dpf", "GSM7924155", "GSM7924155: itgavKO gut3; Danio rerio; RNA Seq", "GSM7924155 r1", "GSM7924155", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz", "fastq fastq", 4146743578.0, 13730939.0, "GSM7924155 r1", "0:151 1:151", "A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387", 151, 151, null, null, 1130002132, 943522869, 958031732, 1115146458, 40387, "SRX22683822", "SRS19677536", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93764, 0.94144, 0.05938, 0.05594, 0.7553, 0.75485, 0.55535, 0.55018, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29045, "SRR26990798", "SRX22683821", "SRS19677535", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "itgavKO gut2", "GSM7924154", null, "source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO gut2", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "gut", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:itgavKO mutant|time:50dpf", "GSM7924154", "GSM7924154: itgavKO gut2; Danio rerio; RNA Seq", "GSM7924154 r1", "GSM7924154", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz", "fastq fastq", 4225756140.0, 13992570.0, "GSM7924154 r1", "0:151 1:151", "A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530", 151, 151, null, null, 1133211420, 974497998, 995876972, 1122129220, 40530, "SRX22683821", "SRS19677535", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.95341, 0.95884, 0.05109, 0.04883, 0.77542, 0.77368, 0.51301, 0.50704, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29046, "SRR26990799", "SRX22683820", "SRS19677534", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "itagvKO gut1", "GSM7924153", null, "source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itagvKO gut1", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "gut", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:itgavKO mutant|time:50dpf", "GSM7924153", "GSM7924153: itagvKO gut1; Danio rerio; RNA Seq", "GSM7924153 r1", "GSM7924153", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz", "fastq fastq", 5954117844.0, 19715622.0, "GSM7924153 r1", "0:151 1:151", "A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859", 151, 151, null, null, 1600496071, 1372939932, 1393534700, 1587094282, 52859, "SRX22683820", "SRS19677534", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.94807, 0.95298, 0.05682, 0.05385, 0.74004, 0.73925, 0.54423, 0.54484, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29575, "SRR27387418", "SRX23063709", "SRS20023731", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Combined Intestine", "combined intestine 6", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T8 6", "T8 6", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A54_1.fastq.gz A54_2.fastq.gz", "fastq fastq", 8459790000.0, 28199300.0, "A54 1.fastq.gz", "0:150 1:150", "A:2287135948;C:1957145280;G:1959338891;T:2256075943;N:93938", 150, 150, null, null, 2287135948, 1957145280, 1959338891, 2256075943, 93938, "SRX23063709", "SRS20023731", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92583, 0.92422, 0.06345, 0.06263, 0.75718, 0.75757, 0.52145, 0.5361, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29576, "SRR27387419", "SRX23063708", "SRS20023730", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Combined Intestine", "combined intestine 5", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T8 5", "T8 5", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A53_1.fastq.gz A53_2.fastq.gz", "fastq fastq", 8302022700.0, 27673409.0, "A53 1.fastq.gz", "0:150 1:150", "A:2241277601;C:1925048164;G:1920142999;T:2215462687;N:91249", 150, 150, null, null, 2241277601, 1925048164, 1920142999, 2215462687, 91249, "SRX23063708", "SRS20023730", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92711, 0.92566, 0.06314, 0.06353, 0.75221, 0.75219, 0.541, 0.53579, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29577, "SRR27387420", "SRX23063707", "SRS20023729", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Combined Intestine", "combined intestine 4", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T8 4", "T8 4", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A49_1.fastq.gz A49_2.fastq.gz", "fastq fastq", 6939976800.0, 23133256.0, "A49 1.fastq.gz", "0:150 1:150", "A:1895013575;C:1589528661;G:1585890890;T:1869466351;N:77323", 150, 150, null, null, 1895013575, 1589528661, 1585890890, 1869466351, 77323, "SRX23063707", "SRS20023729", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92632, 0.92542, 0.06323, 0.06265, 0.75588, 0.75722, 0.55002, 0.55324, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29578, "SRR27387421", "SRX23063706", "SRS20023728", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Combined Intestine", "combined intestine 3", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T8 3", "T8 3", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A44_1.fastq.gz A44_2.fastq.gz", "fastq fastq", 9116379900.0, 30387933.0, "A44 1.fastq.gz", "0:150 1:150", "A:2462347514;C:2113718621;G:2112401730;T:2427812186;N:99849", 150, 150, null, null, 2462347514, 2113718621, 2112401730, 2427812186, 99849, "SRX23063706", "SRS20023728", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.93154, 0.92882, 0.06321, 0.06277, 0.75499, 0.75519, 0.54224, 0.542, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29579, "SRR27387422", "SRX23063705", "SRS20023727", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Combined Intestine", "combined intestine 2", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T8 2", "T8 2", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A43_1.fastq.gz A43_2.fastq.gz", "fastq fastq", 7681997100.0, 25606657.0, "A43 1.fastq.gz", "0:150 1:150", "A:2098281007;C:1758609887;G:1757658923;T:2067364339;N:82944", 150, 150, null, null, 2098281007, 1758609887, 1757658923, 2067364339, 82944, "SRX23063705", "SRS20023727", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92257, 0.92131, 0.07154, 0.07125, 0.74769, 0.74712, 0.52352, 0.51843, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29580, "SRR27387423", "SRX23063704", "SRS20023726", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Combined Intestine", "combined intestine 1", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T8 1", "T8 1", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A29_1.fastq.gz A29_2.fastq.gz", "fastq fastq", 8869294500.0, 29564315.0, "A29 1.fastq.gz", "0:150 1:150", "A:2411657291;C:2043119196;G:2038118093;T:2376336869;N:63051", 150, 150, null, null, 2411657291, 2043119196, 2038118093, 2376336869, 63051, "SRX23063704", "SRS20023726", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.9293, 0.93157, 0.06846, 0.06859, 0.75138, 0.75209, 0.54348, 0.54178, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29582, "SRR27387425", "SRX23063702", "SRS20023724", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Nanoplastics Intestine", "nps intestine 5", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T7 5", "T7 5", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A51_1.fastq.gz A51_2.fastq.gz", "fastq fastq", 8229865500.0, 27432885.0, "A51 1.fastq.gz", "0:150 1:150", "A:2239224965;C:1891494000;G:1890511233;T:2208544358;N:90944", 150, 150, null, null, 2239224965, 1891494000, 1890511233, 2208544358, 90944, "SRX23063702", "SRS20023724", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.9282, 0.92676, 0.06786, 0.06815, 0.74566, 0.74673, 0.54961, 0.55067, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29583, "SRR27387426", "SRX23063701", "SRS20023723", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Nanoplastics Intestine", "nps intestine 4", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T7 4", "T7 4", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A50_1.fastq.gz A50_2.fastq.gz", "fastq fastq", 8549274300.0, 28497581.0, "A50 1.fastq.gz", "0:150 1:150", "A:2321938070;C:1971518879;G:1967040023;T:2288683614;N:93714", 150, 150, null, null, 2321938070, 1971518879, 1967040023, 2288683614, 93714, "SRX23063701", "SRS20023723", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.93231, 0.93126, 0.06361, 0.06304, 0.7527, 0.75211, 0.48289, 0.48336, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29584, "SRR27387427", "SRX23063700", "SRS20023722", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Nanoplastics Intestine", "nps intestine 3", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T7 3", "T7 3", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A48_1.fastq.gz A48_2.fastq.gz", "fastq fastq", 8065026000.0, 26883420.0, "A48 1.fastq.gz", "0:150 1:150", "A:2177870889;C:1870003683;G:1870725132;T:2146337507;N:88789", 150, 150, null, null, 2177870889, 1870003683, 1870725132, 2146337507, 88789, "SRX23063700", "SRS20023722", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92891, 0.92753, 0.05842, 0.05778, 0.71991, 0.72009, 0.51653, 0.51675, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29585, "SRR27387428", "SRX23063699", "SRS20023721", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Nanoplastics Intestine", "nps intestine 2", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T7 2", "T7 2", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A42_1.fastq.gz A42_2.fastq.gz", "fastq fastq", 8391356700.0, 27971189.0, "A42 1.fastq.gz", "0:150 1:150", "A:2247673277;C:1962692430;G:1966871884;T:2214026582;N:92527", 150, 150, null, null, 2247673277, 1962692430, 1966871884, 2214026582, 92527, "SRX23063699", "SRS20023721", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.93153, 0.93045, 0.05902, 0.05934, 0.75424, 0.75546, 0.548, 0.54354, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29586, "SRR27387429", "SRX23063698", "SRS20023720", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Nanoplastics Intestine", "nps intestine 1", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps intestine replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T7 1", "T7 1", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A31_1.fastq.gz A31_2.fastq.gz", "fastq fastq", 8236557000.0, 27455190.0, "A31 1.fastq.gz", "0:150 1:150", "A:2204148101;C:1929010419;G:1925723147;T:2177582914;N:92419", 150, 150, null, null, 2204148101, 1929010419, 1925723147, 2177582914, 92419, "SRX23063698", "SRS20023720", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.93739, 0.93581, 0.06216, 0.06176, 0.75057, 0.75049, 0.54176, 0.53414, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29587, "SRR27387430", "SRX23063697", "SRS20023719", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "6PPDQ Intestine", "6ppdq intestine 6", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T6 6", "T6 6", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A56_1.fastq.gz A56_2.fastq.gz", "fastq fastq", 6435464400.0, 21451548.0, "A56 1.fastq.gz", "0:150 1:150", "A:1748400934;C:1486171533;G:1481023797;T:1719795546;N:72590", 150, 150, null, null, 1748400934, 1486171533, 1481023797, 1719795546, 72590, "SRX23063697", "SRS20023719", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92722, 0.92559, 0.0729, 0.07288, 0.74288, 0.74343, 0.53587, 0.52589, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29588, "SRR27387431", "SRX23063696", "SRS20023718", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "6PPDQ Intestine", "6ppdq intestine 5", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T6 5", "T6 5", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A40_1.fastq.gz A40_2.fastq.gz", "fastq fastq", 8749914000.0, 29166380.0, "A40 1.fastq.gz", "0:150 1:150", "A:2338416402;C:2051360445;G:2055480569;T:2304561447;N:95137", 150, 150, null, null, 2338416402, 2051360445, 2055480569, 2304561447, 95137, "SRX23063696", "SRS20023718", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.94523, 0.9504, 0.03896, 0.03887, 0.80661, 0.80728, 0.46402, 0.45996, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29589, "SRR27387432", "SRX23063695", "SRS20023717", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "6PPDQ Intestine", "6ppdq intestine 4", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T6 4", "T6 4", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A39_1.fastq.gz A39_2.fastq.gz", "fastq fastq", 8140938300.0, 27136461.0, "A39 1.fastq.gz", "0:150 1:150", "A:2198617601;C:1888830697;G:1887283102;T:2166117857;N:89043", 150, 150, null, null, 2198617601, 1888830697, 1887283102, 2166117857, 89043, "SRX23063695", "SRS20023717", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92636, 0.92532, 0.05883, 0.0588, 0.71689, 0.71593, 0.52397, 0.5214, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29590, "SRR27387433", "SRX23063694", "SRS20023716", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "6PPDQ Intestine", "6ppdq intestine 3", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T6 3", "T6 3", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A35_1.fastq.gz A35_2.fastq.gz", "fastq fastq", 6912319200.0, 23041064.0, "A35 1.fastq.gz", "0:150 1:150", "A:1895216825;C:1576630157;G:1574441195;T:1865953455;N:77568", 150, 150, null, null, 1895216825, 1576630157, 1574441195, 1865953455, 77568, "SRX23063694", "SRS20023716", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92983, 0.92816, 0.072, 0.07173, 0.76601, 0.76615, 0.55997, 0.55562, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29591, "SRR27387434", "SRX23063693", "SRS20023715", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "6PPDQ Intestine", "6ppdq intestine 2", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T6 2", "T6 2", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A34_1.fastq.gz A34_2.fastq.gz", "fastq fastq", 7279802100.0, 24266007.0, "A34 1.fastq.gz", "0:150 1:150", "A:1989158951;C:1663891494;G:1668311413;T:1958359476;N:80766", 150, 150, null, null, 1989158951, 1663891494, 1668311413, 1958359476, 80766, "SRX23063693", "SRS20023715", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92923, 0.92655, 0.06821, 0.068, 0.74042, 0.74128, 0.54366, 0.54276, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29593, "SRR27387436", "SRX23063691", "SRS20023713", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "6PPDQ Intestine", "6ppdq intestine 1", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq intestine replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T6 1", "T6 1", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A30_1.fastq.gz A30_2.fastq.gz", "fastq fastq", 7219947600.0, 24066492.0, "A30 1.fastq.gz", "0:150 1:150", "A:1901354175;C:1717600917;G:1716606554;T:1884305293;N:80661", 150, 150, null, null, 1901354175, 1717600917, 1716606554, 1884305293, 80661, "SRX23063691", "SRS20023713", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.93375, 0.93214, 0.05513, 0.05567, 0.74759, 0.74698, 0.5475, 0.54855, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29594, "SRR27387437", "SRX23063690", "SRS20023712", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Control Intestine", "control intestine 6", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T5 6", "T5 6", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A46_1.fastq.gz A46_2.fastq.gz", "fastq fastq", 8509361100.0, 28364537.0, "A46 1.fastq.gz", "0:150 1:150", "A:2341600956;C:1932495972;G:1930461855;T:2304710926;N:91391", 150, 150, null, null, 2341600956, 1932495972, 1930461855, 2304710926, 91391, "SRX23063690", "SRS20023712", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92542, 0.92408, 0.07033, 0.06986, 0.77234, 0.77199, 0.55246, 0.55942, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29595, "SRR27387438", "SRX23063689", "SRS20023711", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Control Intestine", "control intestine 5", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T5 5", "T5 5", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A45_1.fastq.gz A45_2.fastq.gz", "fastq fastq", 7856294100.0, 26187647.0, "A45 1.fastq.gz", "0:150 1:150", "A:2129077180;C:1813666476;G:1813868805;T:2099595491;N:86148", 150, 150, null, null, 2129077180, 1813666476, 1813868805, 2099595491, 86148, "SRX23063689", "SRS20023711", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.93087, 0.92866, 0.06398, 0.06358, 0.75481, 0.75597, 0.55424, 0.55289, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29596, "SRR27387439", "SRX23063688", "SRS20023710", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Control Intestine", "control intestine 4", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T5 4", "T5 4", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A38_1.fastq.gz A38_2.fastq.gz", "fastq fastq", 8039208600.0, 26797362.0, "A38 1.fastq.gz", "0:150 1:150", "A:2201215819;C:1836215616;G:1833348507;T:2168337651;N:91007", 150, 150, null, null, 2201215819, 1836215616, 1833348507, 2168337651, 91007, "SRX23063688", "SRS20023710", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.9219, 0.91957, 0.0702, 0.06947, 0.76343, 0.76493, 0.55355, 0.54863, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29597, "SRR27387440", "SRX23063687", "SRS20023709", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Control Intestine", "control intestine 3", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T5 3", "T5 3", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A37_1.fastq.gz A37_2.fastq.gz", "fastq fastq", 8253642600.0, 27512142.0, "A37 1.fastq.gz", "0:150 1:150", "A:2254958000;C:1889478281;G:1886099650;T:2223014303;N:92366", 150, 150, null, null, 2254958000, 1889478281, 1886099650, 2223014303, 92366, "SRX23063687", "SRS20023709", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92632, 0.92477, 0.06268, 0.06279, 0.76719, 0.76682, 0.53773, 0.53566, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29598, "SRR27387441", "SRX23063686", "SRS20023708", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Control Intestine", "control intestine 2", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T5 2", "T5 2", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A33_1.fastq.gz A33_2.fastq.gz", "fastq fastq", 8276959500.0, 27589865.0, "A33 1.fastq.gz", "0:150 1:150", "A:2244800716;C:1909951370;G:1909130637;T:2212988991;N:87786", 150, 150, null, null, 2244800716, 1909951370, 1909130637, 2212988991, 87786, "SRX23063686", "SRS20023708", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.93248, 0.93089, 0.06402, 0.06475, 0.701, 0.7012, 0.53585, 0.53722, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [29599, "SRR27387442", "SRX23063685", "SRS20023707", "SRP480720", "PRJNA1059246", "Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish", "PRJNA1059246", "Other", "Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves  TWPs contain many harmful chemicals  including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone  which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However  we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.", null, null, null, "Control Intestine", "control intestine 1", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control intestine replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "T5 1", "T5 1", "PCR enrichment of adaptor ligated DNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP480720", null, null, "A32_1.fastq.gz A32_2.fastq.gz", "fastq fastq", 7955418900.0, 26518063.0, "A32 1.fastq.gz", "0:150 1:150", "A:2236485440;C:1768380410;G:1765867470;T:2184596828;N:88752", 150, 150, null, null, 2236485440, 1768380410, 1765867470, 2184596828, 88752, "SRX23063685", "SRS20023707", "SRA1777576", "Nord University|Faculty of Biosciences and Aquaculture", "Nord University", 2, 0.92662, 0.92301, 0.071, 0.07061, 0.75207, 0.75158, 0.53095, 0.54507, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2023-12-30", "Adult", "Adult", "Gut", "Digestive System"], [32923, "SRR29498567", "SRX25008885", "SRS21709104", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F2g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F2g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "10", "10", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F2g_R2.fq.gz F2g_R1.fq.gz", "fastq fastq", 9101949000.0, 30339830.0, "F2g R1.fq.gz", "0:150 1:150", "A:2052853923;C:2394247721;G:2773304460;T:1881440199;N:102697", 150, 150, null, null, 2052853923, 2394247721, 2773304460, 1881440199, 102697, "SRX25008885", "SRS21709104", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.65449, 0.37434, 0.04313, 0.12258, 0.99519, 0.99527, 0.61425, 0.56139, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32924, "SRR29498568", "SRX25008884", "SRS21709103", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F1g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F1g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "09", "09", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F1g_R1.fq.gz F1g_R2.fq.gz", "fastq fastq", 8132653500.0, 27108845.0, "F1g R1.fq.gz", "0:150 1:150", "A:1811779602;C:2095863397;G:2529881799;T:1695036688;N:92014", 150, 150, null, null, 1811779602, 2095863397, 2529881799, 1695036688, 92014, "SRX25008884", "SRS21709103", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.53909, 0.24181, 0.01966, 0.04797, 0.99598, 0.99624, 0.59302, 0.62038, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32931, "SRR29498575", "SRX25008877", "SRS21709096", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M2g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M2g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "12", "12", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M2g_R1.fq.gz M2g_R2.fq.gz", "fastq fastq", 7106243100.0, 23687477.0, "M2g R1.fq.gz", "0:150 1:150", "A:1567154123;C:1866065312;G:2213286944;T:1459656676;N:80045", 150, 150, null, null, 1567154123, 1866065312, 2213286944, 1459656676, 80045, "SRX25008877", "SRS21709096", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.56476, 0.25026, 0.02259, 0.04481, 0.99667, 0.99701, 0.63277, 0.65693, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32932, "SRR29498576", "SRX25008876", "SRS21709095", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M1g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M1g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "11", "11", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M1g_R2.fq.gz M1g_R1.fq.gz", "fastq fastq", 7351182000.0, 24503940.0, "M1g R1.fq.gz", "0:150 1:150", "A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321", 150, 150, null, null, 1623685246, 1858847576, 2315396486, 1553169371, 83321, "SRX25008876", "SRS21709095", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96004, 0.21521, 0.16113, 0.04578, 0.92431, 0.99143, 0.61867, 0.63432, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [33351, "SRR30125634", "SRX25595192", "SRS22245033", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "SBM1 3", "GSM8439539", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "SBM1 3", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439539", "GSM8439539: SBM1 3; Danio rerio; RNA Seq", "GSM8439539 r1", "GSM8439539", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "SBM1-3.R1.fq.gz SBM1-3.R2.fq.gz", "fastq fastq", 6920938402.0, 24030624.0, "GSM8439539 r1", "0:144.00 1:144.00", "A:1848518187;C:1602695225;G:1609135376;T:1860572175;N:17439", 144, 144, null, null, 1848518187, 1602695225, 1609135376, 1860572175, 17439, "SRX25595192", "SRS22245033", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33352, "SRR30125635", "SRX25595191", "SRS22245032", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "SBM1 2", "GSM8439538", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "SBM1 2", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439538", "GSM8439538: SBM1 2; Danio rerio; RNA Seq", "GSM8439538 r1", "GSM8439538", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "SBM1-2.R1.fq.gz SBM1-2.R2.fq.gz", "fastq fastq", 6873386097.0, 23812133.0, "GSM8439538 r1", "0:144.32 1:144.33", "A:1794801562;C:1631426136;G:1638460090;T:1808681001;N:17308", 144, 144, null, null, 1794801562, 1631426136, 1638460090, 1808681001, 17308, "SRX25595191", "SRS22245032", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33353, "SRR30125636", "SRX25595190", "SRS22245031", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "SBM1 1", "GSM8439537", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "SBM1 1", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439537", "GSM8439537: SBM1 1; Danio rerio; RNA Seq", "GSM8439537 r1", "GSM8439537", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "SBM1-1.R1.fq.gz SBM1-1.R2.fq.gz", "fastq fastq", 6893638362.0, 23881631.0, "GSM8439537 r1", "0:144.33 1:144.33", "A:1801507713;C:1634518350;G:1642455999;T:1815139080;N:17220", 144, 144, null, null, 1801507713, 1634518350, 1642455999, 1815139080, 17220, "SRX25595190", "SRS22245031", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33354, "SRR30125637", "SRX25595189", "SRS22245030", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "FM1 3", "GSM8439536", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "FM1 3", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439536", "GSM8439536: FM1 3; Danio rerio; RNA Seq", "GSM8439536 r1", "GSM8439536", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "FM1-3.R1.fq.gz FM1-3.R2.fq.gz", "fastq fastq", 6926890624.0, 24044310.0, "GSM8439536 r1", "0:144.04 1:144.05", "A:1814868011;C:1638590076;G:1645410775;T:1828004537;N:17225", 144, 144, null, null, 1814868011, 1638590076, 1645410775, 1828004537, 17225, "SRX25595189", "SRS22245030", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33355, "SRR30125638", "SRX25595188", "SRS22245029", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "FM1 2", "GSM8439535", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "FM1 2", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439535", "GSM8439535: FM1 2; Danio rerio; RNA Seq", "GSM8439535 r1", "GSM8439535", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "FM1-2.R1.fq.gz FM1-2.R2.fq.gz", "fastq fastq", 6932329149.0, 24050700.0, "GSM8439535 r1", "0:144.12 1:144.12", "A:1821635965;C:1634568957;G:1641356498;T:1834750114;N:17615", 144, 144, null, null, 1821635965, 1634568957, 1641356498, 1834750114, 17615, "SRX25595188", "SRS22245029", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33356, "SRR30125639", "SRX25595187", "SRS22245028", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "FM1 1", "GSM8439534", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "FM1 1", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439534", "GSM8439534: FM1 1; Danio rerio; RNA Seq", "GSM8439534 r1", "GSM8439534", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "FM1-1.R1.fq.gz FM1-1.R2.fq.gz", "fastq fastq", 6915521492.0, 24044109.0, "GSM8439534 r1", "0:143.81 1:143.81", "A:1851629842;C:1595942468;G:1602547587;T:1865384194;N:17401", 143, 143, null, null, 1851629842, 1595942468, 1602547587, 1865384194, 17401, "SRX25595187", "SRS22245028", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33357, "SRR30125640", "SRX25595186", "SRS22245027", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "D3 4 3", "GSM8439533", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "D3 4 3", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439533", "GSM8439533: D3 4 3; Danio rerio; RNA Seq", "GSM8439533 r1", "GSM8439533", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "D3-4-3.R1.fq.gz D3-4-3.R2.fq.gz", "fastq fastq", 6934859246.0, 24095045.0, "GSM8439533 r1", "0:143.91 1:143.91", "A:1815846879;C:1641161510;G:1648091770;T:1829741658;N:17429", 143, 143, null, null, 1815846879, 1641161510, 1648091770, 1829741658, 17429, "SRX25595186", "SRS22245027", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33358, "SRR30125641", "SRX25595185", "SRS22245026", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "D3 4 2", "GSM8439532", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "D3 4 2", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439532", "GSM8439532: D3 4 2; Danio rerio; RNA Seq", "GSM8439532 r1", "GSM8439532", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "D3-4-2.R1.fq.gz D3-4-2.R2.fq.gz", "fastq fastq", 7053487385.0, 24519028.0, "GSM8439532 r1", "0:143.83 1:143.84", "A:1888591272;C:1630003556;G:1636509489;T:1898365125;N:17943", 143, 143, null, null, 1888591272, 1630003556, 1636509489, 1898365125, 17943, "SRX25595185", "SRS22245026", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33359, "SRR30125642", "SRX25595184", "SRS22245025", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin  mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics  \u00df  \u00df Dimethylacryloyl shikonin  mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group  the SBM group  andthe  D3 group  with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "D3 4 1", "GSM8439531", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "D3 4 1", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439531", "GSM8439531: D3 4 1; Danio rerio; RNA Seq", "GSM8439531 r1", "GSM8439531", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz", "fastq fastq", 6996797279.0, 24229469.0, "GSM8439531 r1", "0:144.38 1:144.39", "A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723", 144, 144, null, null, 1841905352, 1647600285, 1654313322, 1852960597, 17723, "SRX25595184", "SRS22245025", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [34137, "SRR31360761", "SRX26734629", "SRS23224778", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "WT3", null, "strain:AB|isolate:WT3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "WT3.fq", "WT3.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "WT3_R1.fq.gz WT3_R2.fq.gz", "fastq fastq", 7045875300.0, 23486251.0, "WT3 R1.fq.gz", "0:150 1:150", "A:1817741681;C:1708030651;G:1712073267;T:1808003621;N:26080", 150, 150, null, null, 1817741681, 1708030651, 1712073267, 1808003621, 26080, "SRX26734629", "SRS23224778", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34138, "SRR31360762", "SRX26734628", "SRS23224777", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "WT2", null, "strain:AB|isolate:WT2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "WT2.fq", "WT2.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "WT2_R1.fq.gz WT2_R2.fq.gz", 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"SRX26734626", "SRS23224775", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "mu3", null, "strain:AB|isolate:mu3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "mu3.fq", "mu3.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "mu3_R1.fq.gz mu3_R2.fq.gz", "fastq fastq", 7304650200.0, 24348834.0, "mu3 R1.fq.gz", "0:150 1:150", "A:1934717193;C:1720864609;G:1730177787;T:1918863192;N:27419", 150, 150, null, null, 1934717193, 1720864609, 1730177787, 1918863192, 27419, "SRX26734626", "SRS23224775", "SRA2015506", "Fudan 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"ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "mu2_R1.fq.gz mu2_R2.fq.gz", "fastq fastq", 7168114200.0, 23893714.0, "mu2 R1.fq.gz", "0:150 1:150", "A:1896004564;C:1692025000;G:1701080897;T:1878977280;N:26459", 150, 150, null, null, 1896004564, 1692025000, 1701080897, 1878977280, 26459, "SRX26734625", "SRS23224774", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34142, "SRR31360766", "SRX26734624", "SRS23224773", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "mu1", null, "strain:AB|isolate:mu1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "mu1.fq", "mu1.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "mu1_R1.fq.gz mu1_R2.fq.gz", "fastq fastq", 7262664600.0, 24208882.0, "mu1 R1.fq.gz", "0:150 1:150", "A:1922666653;C:1711620445;G:1720530432;T:1907824480;N:22590", 150, 150, null, null, 1922666653, 1711620445, 1720530432, 1907824480, 22590, "SRX26734624", "SRS23224773", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34491, "SRR31852177", "SRX27211969", "SRS23661292", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  BG  rep3", "GSM8703891", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  BG  rep3", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7", "GSM8703891", "GSM8703891: Zebrafish  BG  rep3; Danio rerio; RNA Seq", "GSM8703891 r1", "GSM8703891", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "BG_3_R1.fastq.gz BG_3_R2.fastq.gz", "fastq fastq", 6899655382.0, 22846541.0, "GSM8703891 r1", "0:151 1:151", "A:1811966008;C:1615713130;G:1645022233;T:1826840592;N:113419", 151, 151, null, null, 1811966008, 1615713130, 1645022233, 1826840592, 113419, "SRX27211969", "SRS23661292", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34492, "SRR31852178", "SRX27211968", "SRS23661291", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  BG  rep2", "GSM8703890", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  BG  rep2", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7", "GSM8703890", "GSM8703890: Zebrafish  BG  rep2; Danio rerio; RNA Seq", "GSM8703890 r1", "GSM8703890", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "BG_2_R1.fastq.gz BG_2_R2.fastq.gz", "fastq fastq", 6320533538.0, 20928919.0, "GSM8703890 r1", "0:151 1:151", "A:1636247942;C:1501072316;G:1530315619;T:1652793962;N:103699", 151, 151, null, null, 1636247942, 1501072316, 1530315619, 1652793962, 103699, "SRX27211968", "SRS23661291", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34493, "SRR31852179", "SRX27211967", "SRS23661290", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  BG  rep1", "GSM8703889", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  BG  rep1", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7", "GSM8703889", "GSM8703889: Zebrafish  BG  rep1; Danio rerio; RNA Seq", "GSM8703889 r1", "GSM8703889", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "BG_1_R1.fastq.gz BG_1_R2.fastq.gz", "fastq fastq", 6720003132.0, 22251666.0, "GSM8703889 r1", "0:151 1:151", "A:1771169227;C:1572565291;G:1597071360;T:1779087569;N:109685", 151, 151, null, null, 1771169227, 1572565291, 1597071360, 1779087569, 109685, "SRX27211967", "SRS23661290", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34494, "SRR31852180", "SRX27211966", "SRS23661289", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  EIB202  rep3", "GSM8703888", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  EIB202  rep3", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7", "GSM8703888", "GSM8703888: Zebrafish  EIB202  rep3; Danio rerio; RNA Seq", "GSM8703888 r1", "GSM8703888", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "EIB202_3_R1.fastq.gz EIB202_3_R2.fastq.gz", "fastq fastq", 6653244824.0, 22030612.0, "GSM8703888 r1", "0:151 1:151", "A:1715767195;C:1587994105;G:1617241387;T:1732132934;N:109203", 151, 151, null, null, 1715767195, 1587994105, 1617241387, 1732132934, 109203, "SRX27211966", "SRS23661289", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34495, "SRR31852181", "SRX27211965", "SRS23661288", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  EIB202  rep2", "GSM8703887", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  EIB202  rep2", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7", "GSM8703887", "GSM8703887: Zebrafish  EIB202  rep2; Danio rerio; RNA Seq", "GSM8703887 r1", "GSM8703887", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "EIB202_2_R1.fastq.gz EIB202_2_R2.fastq.gz", "fastq fastq", 7203983198.0, 23854249.0, "GSM8703887 r1", "0:151 1:151", "A:1847641462;C:1731806146;G:1763208826;T:1861209998;N:116766", 151, 151, null, null, 1847641462, 1731806146, 1763208826, 1861209998, 116766, "SRX27211965", "SRS23661288", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34496, "SRR31852182", "SRX27211964", "SRS23661287", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  EIB202  rep1", "GSM8703886", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  EIB202  rep1", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7", "GSM8703886", "GSM8703886: Zebrafish  EIB202  rep1; Danio rerio; RNA Seq", "GSM8703886 r1", "GSM8703886", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "EIB202_1_R1.fastq.gz EIB202_1_R2.fastq.gz", "fastq fastq", 6634863292.0, 21969746.0, "GSM8703886 r1", "0:151 1:151", "A:1708949626;C:1589664250;G:1615939413;T:1720201415;N:108588", 151, 151, null, null, 1708949626, 1589664250, 1615939413, 1720201415, 108588, "SRX27211964", "SRS23661287", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34497, "SRR31852183", "SRX27211963", "SRS23661286", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  mock  rep3", "GSM8703885", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  mock  rep3", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7", "GSM8703885", "GSM8703885: Zebrafish  mock  rep3; Danio rerio; RNA Seq", "GSM8703885 r1", "GSM8703885", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "Mock_3_R1.fastq.gz Mock_3_R2.fastq.gz", "fastq fastq", 6938479596.0, 22975098.0, "GSM8703885 r1", "0:151 1:151", "A:1771058080;C:1670207033;G:1705035413;T:1792066207;N:112863", 151, 151, null, null, 1771058080, 1670207033, 1705035413, 1792066207, 112863, "SRX27211963", "SRS23661286", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34498, "SRR31852184", "SRX27211962", "SRS23661285", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  mock  rep2", "GSM8703884", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  mock  rep2", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7", "GSM8703884", "GSM8703884: Zebrafish  mock  rep2; Danio rerio; RNA Seq", "GSM8703884 r1", "GSM8703884", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "Mock_2_R1.fastq.gz Mock_2_R2.fastq.gz", "fastq fastq", 7374531658.0, 24418979.0, "GSM8703884 r1", "0:151 1:151", "A:1885070518;C:1779385428;G:1810157081;T:1899798486;N:120145", 151, 151, null, null, 1885070518, 1779385428, 1810157081, 1899798486, 120145, "SRX27211962", "SRS23661285", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [34499, "SRR31852185", "SRX27211961", "SRS23661284", "SRP554424", "PRJNA1204310", "Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish", "GSE285528", "Transcriptome Analysis", "Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However  whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here  through establishing an in vivo \u00df glucan training and E. piscicida infection model in zebrafish  we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover  we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore  we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together  our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis  and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS  or \u00df glucan trained at Day 7 post secondary E. piscicida infection", null, null, null, "Zebrafish  mock  rep1", "GSM8703883", null, "source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing", "Zebrafish  mock  rep1", "Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample", "Intestine", "10 \u00b5L yeast derived \u03b2 glucan 10 mg/mL was intraperitoneally injected i.p.  and post resting for 5 days  5 \u00b5L E. piscicida2 \u00d7 106 CFU/mL was challenged with through rectal injection", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", "Three to six mpf AB line zebrafish were maintained at 27 \u00b1 1 \u00b0C and under a controlled light/dark cycle 14 h light/10 h dark.", "tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7", "GSM8703883", "GSM8703883: Zebrafish  mock  rep1; Danio rerio; RNA Seq", "GSM8703883 r1", "GSM8703883", "1", "The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP554424", null, null, "Mock_1_R1.fastq.gz Mock_1_R2.fastq.gz", "fastq fastq", 6563252448.0, 21732624.0, "GSM8703883 r1", "0:151 1:151", "A:1759569033;C:1514211809;G:1536003223;T:1753362072;N:106311", 151, 151, null, null, 1759569033, 1514211809, 1536003223, 1753362072, 106311, "SRX27211961", "SRS23661284", "SRA2042566", "Ahua lab, East China University of Science and Technology", "Ahua lab, East China University of Science and Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-12-30", "Adult", "Adult", "Gut", "Digestive System"], [38059, "SRR1524245", "SRX661010", "SRS665985", "SRP044781", "PRJNA255848", "Danio rerio Transcriptome", "PRJNA255848", "Transcriptome Analysis", "Transcriptome analysis of 12 zebrafish tissues", "parent bioproject:PRJNA255979", "pubmed:27189481", "Zebrafish intestine", "Zebrafish intestine", "F Dr 9", null, "strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish intestine", "F Dr 9", "F Dr 9", "Total RNA was qualified using an Agilent BioAnalyzer and 1 \u00b5g was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP044781", null, null, "F_Dr_9_GCCAAT_L005_R2.fastq.gz F_Dr_9_GCCAAT_L005_R1.fastq.gz", "fastq fastq", 8637468200.0, 43187341.0, "F Dr 9 files", "0:100 1:100", "A:2270309093;C:2039596980;G:2056249938;T:2263331787;N:7980402", 100, 100, null, null, 2270309093, 2039596980, 2056249938, 2263331787, 7980402, "SRX661010", "SRS665985", "SRA176464", "INRA|Fish Physiology and Genomics", "INRA PhyloFish", 2, 0.94661, 0.94511, 0.06033, 0.06049, 0.75743, 0.75747, 0.43604, 0.43901, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "France", "2015-07-24", "Adult", "Adult", "Gut", "Digestive System"], [38269, "SRR1609746", "SRX730399", "SRS719620", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "intestine10", "GSM1523041", null, "source name:intestine|tissue:intestine|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "intestine10", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "intestine", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:intestine|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523041", "GSM1523041: intestine10; Danio rerio; RNA Seq", "GSM1523041", null, "1", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523041", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "intestine10_2.fq.gz intestine10_1.fq.gz", "fastq fastq", 3638953000.0, 18194765.0, "GSM1523041 r1", "0:100 1:100", "A:944286084;C:877180113;G:870958371;T:946463708;N:64724", 100, 100, null, null, 944286084, 877180113, 870958371, 946463708, 64724, "SRX730399", "SRS719620", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.95871, 0.95555, 0.03654, 0.03737, 0.77546, 0.77597, 0.49972, 0.50867, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Gut", "Digestive System"], [38270, "SRR1609745", "SRX730398", "SRS719619", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "intestine18", "GSM1523040", null, "source name:intestine|tissue:intestine|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "intestine18", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "intestine", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:intestine|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523040", "GSM1523040: intestine18; Danio rerio; RNA Seq", "GSM1523040", null, "1", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523040", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "intestine18_1.fq.gz intestine18_2.fq.gz", "fastq fastq", 3870426800.0, 19352134.0, "GSM1523040 r1", "0:100 1:100", "A:1034436410;C:900862332;G:899347839;T:1035707094;N:73125", 100, 100, null, null, 1034436410, 900862332, 899347839, 1035707094, 73125, "SRX730398", "SRS719619", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.93279, 0.92997, 0.0455, 0.04571, 0.76152, 0.76228, 0.44545, 0.44882, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Gut", "Digestive System"], [38271, "SRR1609744", "SRX730397", "SRS719618", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "intestine28", "GSM1523039", null, "source name:intestine|tissue:intestine|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "intestine28", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "intestine", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:intestine|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523039", "GSM1523039: intestine28; Danio rerio; RNA Seq", "GSM1523039", null, "1", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523039", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "intestine28_1.fq.gz intestine28_2.fq.gz", "fastq fastq", 3710350200.0, 18551751.0, "GSM1523039 r1", "0:100 1:100", "A:987499090;C:870092319;G:865419689;T:987267641;N:71461", 100, 100, null, null, 987499090, 870092319, 865419689, 987267641, 71461, "SRX730397", "SRS719618", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.94613, 0.94058, 0.04736, 0.04784, 0.7599, 0.76288, 0.51653, 0.51797, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Gut", "Digestive System"], [41844, "SRR5259817", "SRX2564548", "SRS1981207", "SRP099850", "PRJNA374872", "Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]", "GSE94933", "Other", "We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish", "parent bioproject:PRJNA374867", "pubmed:28850571", null, "zIEC3 mRNA", "GSM2492108", null, "tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "zIEC3 mRNA", "Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information", "Intestinal Epithelial Cells RNA seq", null, "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets", "strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "GSM2492108", "GSM2492108: zIEC3 mRNA; Danio rerio; RNA Seq", "GSM2492108", null, "1", "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "GEO Accession:GSM2492108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099850", null, null, "ZIEC3_GCCAAT_L001_R2_001.fastq.gz ZIEC3_GCCAAT_L001_R1_001.fastq.gz", "fastq fastq", 2644689216.0, 27548846.0, "GSM2492108 r1", "0:48 1:48", "A:687890725;C:632255900;G:620389531;T:703494916;N:658144", 48, 48, null, null, 687890725, 632255900, 620389531, 703494916, 658144, "SRX2564548", "SRS1981207", "SRA538156", "GEO", "John Rawls, Duke University", 2, 0.87587, 0.87862, 0.06582, 0.06632, 0.73931, 0.73878, 0.53496, 0.53653, 48, 48, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-02-15", "Adult", "Adult", "Gut", "Digestive System"], [41845, "SRR5259816", "SRX2564547", "SRS1981208", "SRP099850", "PRJNA374872", "Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]", "GSE94933", "Other", "We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish", "parent bioproject:PRJNA374867", "pubmed:28850571", null, "zIEC2 mRNA", "GSM2492107", null, "tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "zIEC2 mRNA", "Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information", "Intestinal Epithelial Cells RNA seq", null, "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets", "strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "GSM2492107", "GSM2492107: zIEC2 mRNA; Danio rerio; RNA Seq", "GSM2492107", null, "1", "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "GEO Accession:GSM2492107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099850", null, null, "ZIEC2_GCCAAT_L005_R1_001.fastq.gz ZIEC2_GCCAAT_L005_R2_001.fastq.gz", "fastq fastq", 1785594816.0, 18599946.0, "GSM2492107 r1", "0:48 1:48", "A:466092820;C:422828003;G:420238032;T:476324795;N:111166", 48, 48, null, null, 466092820, 422828003, 420238032, 476324795, 111166, "SRX2564547", "SRS1981208", "SRA538156", "GEO", "John Rawls, Duke University", 2, 0.85545, 0.86359, 0.08337, 0.08488, 0.74635, 0.74677, 0.52663, 0.53064, 48, 48, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-02-15", "Adult", "Adult", "Gut", "Digestive System"], [41846, "SRR5259815", "SRX2564546", "SRS1981206", "SRP099850", "PRJNA374872", "Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]", "GSE94933", "Other", "We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish", "parent bioproject:PRJNA374867", "pubmed:28850571", null, "zIEC1 mRNA", "GSM2492106", null, "tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "zIEC1 mRNA", "Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information", "Intestinal Epithelial Cells RNA seq", null, "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets", "strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "GSM2492106", "GSM2492106: zIEC1 mRNA; Danio rerio; RNA Seq", "GSM2492106", null, "1", "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "GEO Accession:GSM2492106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099850", null, null, "ZIEC1_CGATGT_L004_R1_001.fastq.gz ZIEC1_CGATGT_L004_R2_001.fastq.gz", "fastq fastq", 1953396576.0, 20347881.0, "GSM2492106 r1", "0:48 1:48", "A:510243495;C:461085497;G:464477553;T:517509152;N:80879", 48, 48, null, null, 510243495, 461085497, 464477553, 517509152, 80879, "SRX2564546", "SRS1981206", "SRA538156", "GEO", "John Rawls, Duke University", 2, 0.87991, 0.88564, 0.09576, 0.0974, 0.74789, 0.74909, 0.54326, 0.54368, 48, 48, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-02-15", "Adult", "Adult", "Gut", "Digestive System"], [44033, "SRR6231893", "SRX3340325", "SRS2641976", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP positive cells", "en GFP positive JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP positive JK r1", "en GFP positive JK r1 fwd", "en GFP positive JK r1 fwd", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFPA_GCCAAT_R1_001.fastq.gz d7phoGFPA_GCCAAT_R2_001.fastq.gz", "fastq fastq", 22618935400.0, 113094677.0, "d7phoGFPA GCCAAT R1 001.fastq.gz", "0:100 1:100", "A:6233619158;C:5097706589;G:5045972110;T:6222785585;N:18851958", 100, 100, null, null, 6233619158, 5097706589, 5045972110, 6222785585, 18851958, "SRX3340325", "SRS2641976", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.91266, 0.9056, 0.16638, 0.16643, 0.68008, 0.68367, 0.48483, 0.48254, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-10-27", "Larval", "Larval", "Gut", "Digestive System"], [44034, "SRR6231894", "SRX3340324", "SRS2641976", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP positive cells", "en GFP positive JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP positive JK r2", "en GFP positive JK r2 fwd", "en GFP positive JK r2 fwd", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFPB_GTGAAA_R2_001.fastq.gz d7phoGFPB_GTGAAA_R1_001.fastq.gz", "fastq fastq", 13753541400.0, 68767707.0, "d7phoGFPB GTGAAA R1 001.fastq.gz", "0:100 1:100", "A:3807602619;C:3077358417;G:3063510819;T:3793560543;N:11509002", 100, 100, null, null, 3807602619, 3077358417, 3063510819, 3793560543, 11509002, "SRX3340324", "SRS2641976", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.90465, 0.89478, 0.20689, 0.2048, 0.68402, 0.68738, 0.4887, 0.48279, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-10-27", "Larval", "Larval", "Gut", "Digestive System"], [44035, "SRR6231895", "SRX3340323", "SRS2641979", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP negative cells", "en GFP negative JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal non neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP negative JK r1", "en GFP negative JK r1 fwd", "en GFP negative JK r1 fwd", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFP-A_ACAGTG_R1_001.fastq.gz d7phoGFP-A_ACAGTG_R2_001.fastq.gz", "fastq fastq", 17591029600.0, 87955148.0, "d7phoGFP A ACAGTG R2 001.fastq.gz", "0:100 1:100", "A:4757105599;C:4046056704;G:4012427038;T:4760767597;N:14672662", 100, 100, null, null, 4757105599, 4046056704, 4012427038, 4760767597, 14672662, "SRX3340323", "SRS2641979", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.91795, 0.92394, 0.12634, 0.12565, 0.69479, 0.68976, 0.50879, 0.5095, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-10-27", "Larval", "Larval", "Gut", "Digestive System"], [44036, "SRR6231897", "SRX3340321", "SRS2641979", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP negative cells", "en GFP negative JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal non neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP negative JK r2", "en GFP negative JK r2 rev", "en GFP negative JK r2 rev", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFP-B_CTTGTA_R1_001.fastq.gz d7phoGFP-B_CTTGTA_R2_001.fastq.gz", "fastq fastq", 21627852000.0, 108139260.0, "d7phoGFP B CTTGTA R2 001.fastq.gz", "0:100 1:100", "A:5802401896;C:5026391965;G:4975450919;T:5805553498;N:18053722", 100, 100, null, null, 5802401896, 5026391965, 4975450919, 5805553498, 18053722, "SRX3340321", "SRS2641979", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.93032, 0.9242, 0.11858, 0.1194, 0.69209, 0.69544, 0.50104, 0.50121, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-02", "Larval", "Larval", "Gut", "Digestive System"], [45031, "SRR6466455", "SRX3556412", "SRS2829760", "SRP128941", "PRJNA428924", "Danio rerio breed:TU Transcriptome or Gene expression", "PRJNA428924", "Transcriptome Analysis", "In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish", null, null, "pooled of 15 intestine of juveniles  at 35 dpf old.", null, "Control 35", null, "breed:TU|age:35 dpf|sex:pooled male and female|tissue:intestine|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish larvae with or without xxx administration", "Ctl 35", "Ctl 35", "Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen  Beijing  China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen  USA. RNA concentration was measured using Qubit  RNA Assay Kit in Qubit  2.0 Flurometer Life Technologies  CA  USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies  CA  USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq  equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP128941", null, null, "ZFGCK_1.fq.gz ZFGCK_2.fq.gz", "fastq fastq", 4031784000.0, 16127136.0, "ZFGCK 2.fq.gz", "0:125 1:125", "A:1069662566;C:940723613;G:944143624;T:1077192856;N:61341", 125, 125, null, null, 1069662566, 940723613, 944143624, 1077192856, 61341, "SRX3556412", "SRS2829760", "SRA646164", "Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis", "Chinese Academy of Agricultural Sciences", 2, 0.93591, 0.9405, 0.06779, 0.06732, 0.72157, 0.72372, 0.53789, 0.52813, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-01-12", "Juvenile", "Juvenile", "Gut", "Digestive System"], [45032, "SRR6466456", "SRX3556411", "SRS2829759", "SRP128941", "PRJNA428924", "Danio rerio breed:TU Transcriptome or Gene expression", "PRJNA428924", "Transcriptome Analysis", "In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish", null, null, "pooled of 15 intestine of juveniles at 35 dpf old with BL23 administration", null, "BL23 35", null, "breed:TU|age:35 dpf|sex:pooled male and female|tissue:intestine|treatment:BL23 administration|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish larvae with or without xxx administration", "BL23 35", "BL23 35", "Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen  Beijing  China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen  USA. RNA concentration was measured using Qubit  RNA Assay Kit in Qubit  2.0 Flurometer Life Technologies  CA  USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies  CA  USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq  equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP128941", null, null, "ZFGBL23_1.fq.gz ZFGBL23_2.fq.gz", "fastq fastq", 3545702250.0, 14182809.0, "ZFGBL23 1.fq.gz", "0:125 1:125", "A:931928697;C:835347026;G:838503871;T:939869548;N:53108", 125, 125, null, null, 931928697, 835347026, 838503871, 939869548, 53108, "SRX3556411", "SRS2829759", "SRA646164", "Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis", "Chinese Academy of Agricultural Sciences", 2, 0.94166, 0.94611, 0.05678, 0.05657, 0.71652, 0.71894, 0.51987, 0.53609, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-01-12", "Juvenile", "Juvenile", "Gut", "Digestive System"], [49070, "SRR7641841", "SRX4505270", "SRS3625663", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 9dpf wt3", "GSM3318287", null, "source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 9dpf wt3", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318287", "GSM3318287: Danio rerio RNAseq intestine 9dpf wt3; Danio rerio; RNA Seq", "GSM3318287", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318287", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt9dpf3_AGTCAA_R2.fastq.gz lane1_BSwt9dpf3_AGTCAA_R1.fastq.gz", "fastq fastq", 2761029656.0, 32104996.0, "GSM3318287 r1", "0:43 1:43", "A:708766648;C:643915678;G:711330854;T:696326829;N:689647", 43, 43, null, null, 708766648, 643915678, 711330854, 696326829, 689647, "SRX4505270", "SRS3625663", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.89599, 0.88107, 0.38979, 0.37161, 0.72523, 0.72705, 0.60581, 0.60845, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49071, "SRR7641840", "SRX4505269", "SRS3625661", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 9dpf wt2", "GSM3318286", null, "source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 9dpf wt2", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318286", "GSM3318286: Danio rerio RNAseq intestine 9dpf wt2; Danio rerio; RNA Seq", "GSM3318286", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318286", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt9dpf2_GGCTAC_R2.fastq.gz lane1_BSwt9dpf2_GGCTAC_R1.fastq.gz", "fastq fastq", 3774884086.0, 43894001.0, "GSM3318286 r1", "0:43 1:43", "A:912580559;C:950011527;G:1000247169;T:911105213;N:939618", 43, 43, null, null, 912580559, 950011527, 1000247169, 911105213, 939618, "SRX4505269", "SRS3625661", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.91348, 0.89692, 0.32028, 0.31, 0.75479, 0.76398, 0.64335, 0.62378, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49072, "SRR7641838", "SRX4505267", "SRS3625659", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 9dpf wt1", "GSM3318285", null, "source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 9dpf wt1", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318285", "GSM3318285: Danio rerio RNAseq intestine 9dpf wt1; Danio rerio; RNA Seq", "GSM3318285", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318285", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt9dpf1_TAGCTT_R2.fastq.gz lane1_BSwt9dpf1_TAGCTT_R1.fastq.gz", "fastq fastq", 2839107938.0, 33012883.0, "GSM3318285 r1", "0:43 1:43", "A:706052485;C:678593541;G:744406061;T:709347067;N:708784", 43, 43, null, null, 706052485, 678593541, 744406061, 709347067, 708784, "SRX4505267", "SRS3625659", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.90142, 0.89053, 0.40928, 0.39461, 0.72622, 0.72768, 0.51721, 0.5385, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49073, "SRR7641837", "SRX4505266", "SRS3625658", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 7dpf wt3", "GSM3318284", null, "source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 7dpf wt3", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318284", "GSM3318284: Danio rerio RNAseq intestine 7dpf wt3; Danio rerio; RNA Seq", "GSM3318284", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318284", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt7dpf3_GATCAG_R1.fastq.gz lane1_BSwt7dpf3_GATCAG_R2.fastq.gz", "fastq fastq", 3032189462.0, 35258017.0, "GSM3318284 r1", "0:43 1:43", "A:728621779;C:727851984;G:867302660;T:707649251;N:763788", 43, 43, null, null, 728621779, 727851984, 867302660, 707649251, 763788, "SRX4505266", "SRS3625658", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.87964, 0.8732, 0.36258, 0.35306, 0.7259, 0.72934, 0.56793, 0.56457, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49074, "SRR7641836", "SRX4505265", "SRS3625657", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 7dpf wt2", "GSM3318283", null, "source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 7dpf wt2", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318283", "GSM3318283: Danio rerio RNAseq intestine 7dpf wt2; Danio rerio; RNA Seq", "GSM3318283", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318283", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt7dpf2_ACTTGA_R2.fastq.gz lane1_BSwt7dpf2_ACTTGA_R1.fastq.gz", "fastq fastq", 2796267812.0, 32514742.0, "GSM3318283 r1", "0:43 1:43", "A:678627733;C:682194336;G:763077086;T:671672090;N:696567", 43, 43, null, null, 678627733, 682194336, 763077086, 671672090, 696567, "SRX4505265", "SRS3625657", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.88818, 0.88174, 0.43784, 0.42578, 0.72531, 0.72417, 0.51845, 0.53225, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49075, "SRR7641834", "SRX4505264", "SRS3625656", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 7dpf wt1", "GSM3318282", null, "source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 7dpf wt1", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318282", "GSM3318282: Danio rerio RNAseq intestine 7dpf wt1; Danio rerio; RNA Seq", "GSM3318282", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318282", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt7dpf1_TTAGGC_R2.fastq.gz lane1_BSwt7dpf1_TTAGGC_R1.fastq.gz", "fastq fastq", 2657998302.0, 30906957.0, "GSM3318282 r1", "0:43 1:43", "A:670335271;C:630669243;G:685436534;T:670905092;N:652162", 43, 43, null, null, 670335271, 630669243, 685436534, 670905092, 652162, "SRX4505264", "SRS3625656", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.87993, 0.87022, 0.42578, 0.40713, 0.69828, 0.70244, 0.54254, 0.55209, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49076, "SRR7641833", "SRX4505263", "SRS3625655", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 5dpf wt3", "GSM3318281", null, "source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 5dpf wt3", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318281", "GSM3318281: Danio rerio RNAseq intestine 5dpf wt3; Danio rerio; RNA Seq", "GSM3318281", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318281", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt5dpf3_CAGATC_R1.fastq.gz lane1_BSwt5dpf3_CAGATC_R2.fastq.gz", "fastq fastq", 3471426378.0, 40365423.0, "GSM3318281 r1", "0:43 1:43", "A:816007186;C:888388842;G:957708559;T:808447064;N:874727", 43, 43, null, null, 816007186, 888388842, 957708559, 808447064, 874727, "SRX4505263", "SRS3625655", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.86569, 0.86483, 0.38669, 0.37568, 0.7277, 0.73148, 0.51986, 0.52105, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49077, "SRR7641832", "SRX4505262", "SRS3625654", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 5dpf wt2", "GSM3318280", null, "source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 5dpf wt2", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318280", "GSM3318280: Danio rerio RNAseq intestine 5dpf wt2; Danio rerio; RNA Seq", "GSM3318280", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318280", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt5dpf2_GCCAAT_R2.fastq.gz lane1_BSwt5dpf2_GCCAAT_R1.fastq.gz", "fastq fastq", 2424100404.0, 28187214.0, "GSM3318280 r1", "0:43 1:43", "A:657799034;C:534330605;G:575770800;T:655604713;N:595252", 43, 43, null, null, 657799034, 534330605, 575770800, 655604713, 595252, "SRX4505262", "SRS3625654", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.85487, 0.83514, 0.56287, 0.53286, 0.69583, 0.69658, 0.54518, 0.55246, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49078, "SRR7641830", "SRX4505261", "SRS3625653", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 5dpf wt1", "GSM3318279", null, "source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 5dpf wt1", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318279", "GSM3318279: Danio rerio RNAseq intestine 5dpf wt1; Danio rerio; RNA Seq", "GSM3318279", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318279", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt5dpf1_ACAGTG_R1.fastq.gz lane1_BSwt5dpf1_ACAGTG_R2.fastq.gz", "fastq fastq", 2258154890.0, 26257615.0, "GSM3318279 r1", "0:43 1:43", "A:568380294;C:542047927;G:584939179;T:562222871;N:564619", 43, 43, null, null, 568380294, 542047927, 584939179, 562222871, 564619, "SRX4505261", "SRS3625653", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.89313, 0.87302, 0.42444, 0.40784, 0.72096, 0.72393, 0.58673, 0.60423, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [52131, "SRR8944754", "SRX5724887", "SRS4662952", "SRP193452", "PRJNA534016", "fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome", "PRJNA534016", "Other", "In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.", null, null, "In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.", "fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome", "intestinal transcriptome sequencing of fabp2 gene KO and WT zebrafish", null, "isolate:fabp2 gene KO and WT zebrafish|dev stage:adult|sex:not collected|tissue:intestine|collected by:Yan Zhao|collection date:2017 10|geo loc name:China: Wuhan city  Hubei province|sample type:tissue sample|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "intestinal transcritome sequencing", "fabp2 gene KO Danio rerio", "fabp2 gene KO Danio rerio", "Total RNAs were extracted from the intestine of experimental fish using Trizol. The construction of the cDNA library and sequencing were performed using Illumina NovaSeq 6000 HiSeq 2000 platform Illumina  CA  USA.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP193452", null, null, "KO1_1.fastq.gz KO2_2.fastq.gz KO2_1.fastq.gz KO1_2.fastq.gz", "fastq fastq fastq fastq", 21269908500.0, 70899695.0, "KO1 1.fastq.gz", "0:150 1:150", "A:5602268133;C:4968099632;G:4965298378;T:5733027255;N:1215102", 150, 150, null, null, 5602268133, 4968099632, 4965298378, 5733027255, 1215102, "SRX5724887", "SRS4662952", "SRA878388", "Huazhong Agricultural University|Fisheries College", "Huazhong Agricultural University", 2, 0.92003, 0.92121, 0.03272, 0.03273, 0.78488, 0.78859, 0.49044, 0.48398, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-04-23", "Adult", "Adult", "Gut", "Digestive System"], [52132, "SRR8944755", "SRX5724886", "SRS4662952", "SRP193452", "PRJNA534016", "fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome", "PRJNA534016", "Other", "In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.", null, null, "In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs  hepatic and serum lipid content in fabp2 gene knockout KO zebrafish  we performed the intestinal transcriptome analysis.", "fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome", "intestinal transcriptome sequencing of fabp2 gene KO and WT zebrafish", null, "isolate:fabp2 gene KO and WT zebrafish|dev stage:adult|sex:not collected|tissue:intestine|collected by:Yan Zhao|collection date:2017 10|geo loc name:China: Wuhan city  Hubei province|sample type:tissue sample|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "intestinal transcritome sequencing", "wild type Danio rerio", "wild type Danio rerio", "Total RNAs were extracted from the intestine of experimental fish using Trizol. The construction of the cDNA library and sequencing were performed using Illumina NovaSeq 6000 HiSeq 2001 platform Illumina  CA  USA.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP193452", null, null, "WT1_1.fastq.gz WT1_2.fastq.gz WT2_1.fastq.gz WT2_2.fastq.gz", "fastq fastq fastq fastq", 23433575100.0, 78111917.0, "WT1 1.fastq.gz", "0:150 1:150", "A:6211885445;C:5476158510;G:5474363796;T:6269801731;N:1365618", 150, 150, null, null, 6211885445, 5476158510, 5474363796, 6269801731, 1365618, "SRX5724886", "SRS4662952", "SRA878388", "Huazhong Agricultural University|Fisheries College", "Huazhong Agricultural University", 2, 0.92141, 0.92214, 0.04124, 0.04142, 0.77664, 0.78182, 0.5318, 0.52116, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-04-23", "Adult", "Adult", "Gut", "Digestive System"], [52338, "SRR9141302", "SRX5914456", "SRS4832644", "SRP199735", "PRJNA545244", "Zebrafish transcriptome data", "PRJNA545244", "Other", "Heavy metals stimulate zebrafish", null, null, null, null, "Drt1 2 aliquot", null, "isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult female gut", "Drt1 2", "Drt1 2", "Gene expression in zebrafish stimulated by heavy metals", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP199735", null, null, "Drt1-2 (pooling35-GCCAAT_HY2FYCCXY_L8_1.fq and pooling35-GCCAAT_HY2FYCCXY_L8_2.fq).gz", "fastq", 4010314800.0, 26735432.0, "Drt1 2 pooling35 GCCAAT HY2FYCCXY L8 1.fq and pooling35 GCCAAT HY2FYCCXY L8 2.fq.gz", "0:0 1:150", "A:1109402697;C:898932519;G:975504514;T:1026302103;N:172967", 0, 150, null, null, 1109402697, 898932519, 975504514, 1026302103, 172967, "SRX5914456", "SRS4832644", "SRA891446", "Kunming University of Science and Technology|College of Life Science", "Kunming University of Science and Technology", 1, 0.92372, null, 0.03616, null, 0.74588, null, 0.49008, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-29", "Adult", "Adult", "Gut", "Digestive System"], [52339, "SRR9141303", "SRX5914455", "SRS4832643", "SRP199735", "PRJNA545244", "Zebrafish transcriptome data", "PRJNA545244", "Other", "Heavy metals stimulate zebrafish", null, null, null, null, "Drt1 3 aliquot", null, "isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult female gut", "Drt1 3", "Drt1 3", "Gene expression in zebrafish stimulated by heavy metals", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP199735", null, null, "Drt1-3 (pooling35-CAGATC_HY2FYCCXY_L8_1.fq and pooling35-CAGATC_HY2FYCCXY_L8_2.fq).gz", "fastq", 3497539200.0, 23316928.0, "Drt1 3 pooling35 CAGATC HY2FYCCXY L8 1.fq and pooling35 CAGATC HY2FYCCXY L8 2.fq.gz", "0:0 1:150", "A:965958483;C:783630086;G:850473225;T:897324973;N:152433", 0, 150, null, null, 965958483, 783630086, 850473225, 897324973, 152433, "SRX5914455", "SRS4832643", "SRA891446", "Kunming University of Science and Technology|College of Life Science", "Kunming University of Science and Technology", 1, 0.92356, null, 0.03568, null, 0.7417, null, 0.48985, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-29", "Adult", "Adult", "Gut", "Digestive System"], [52340, "SRR9141304", "SRX5914454", "SRS4832642", "SRP199735", "PRJNA545244", "Zebrafish transcriptome data", "PRJNA545244", "Other", "Heavy metals stimulate zebrafish", null, null, null, null, "Drck3 aliquot", null, "isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult female gut", "Drck3", "Drck3", "Gene expression in zebrafish stimulated by heavy metals", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP199735", null, null, "Drck3 (pooling35-TAGCTT_HY2FYCCXY_L8_1.fq and pooling35-TAGCTT_HY2FYCCXY_L8_2.fq).gz", "fastq", 4199739150.0, 27998261.0, "Drck3 pooling35 TAGCTT HY2FYCCXY L8 1.fq and pooling35 TAGCTT HY2FYCCXY L8 2.fq.gz", "0:0 1:150", "A:1173351504;C:941132248;G:1019438569;T:1065634216;N:182613", 0, 150, null, null, 1173351504, 941132248, 1019438569, 1065634216, 182613, "SRX5914454", "SRS4832642", "SRA891446", "Kunming University of Science and Technology|College of Life Science", "Kunming University of Science and Technology", 1, 0.92976, null, 0.0377, null, 0.71709, null, 0.48608, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-29", "Adult", "Adult", "Gut", "Digestive System"], [52341, "SRR9141305", "SRX5914453", "SRS4832641", "SRP199735", "PRJNA545244", "Zebrafish transcriptome data", "PRJNA545244", "Other", "Heavy metals stimulate zebrafish", null, null, null, null, "Drt1 1 aliquot", null, "isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult female gut", "Drt1 1", "Drt1 1", "Gene expression in zebrafish stimulated by heavy metals", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP199735", null, null, "Drt1-1 (pooling35-ACAGTG_HY2FYCCXY_L8_1.fq and pooling35-ACAGTG_HY2FYCCXY_L8_2.fq).gz", "fastq", 3657007500.0, 24380050.0, "Drt1 1 pooling35 ACAGTG HY2FYCCXY L8 1.fq and pooling35 ACAGTG HY2FYCCXY L8 2.fq.gz", "0:150 1:0", "A:963212012;C:848159609;G:822435259;T:1023096853;N:103767", 150, 0, null, null, 963212012, 848159609, 822435259, 1023096853, 103767, "SRX5914453", "SRS4832641", "SRA891446", "Kunming University of Science and Technology|College of Life Science", "Kunming University of Science and Technology", 1, 0.92318, null, 0.03725, null, 0.72997, null, 0.48413, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-29", "Adult", "Adult", "Gut", "Digestive System"], [52342, "SRR9141306", "SRX5914452", "SRS4832640", "SRP199735", "PRJNA545244", "Zebrafish transcriptome data", "PRJNA545244", "Other", "Heavy metals stimulate zebrafish", null, null, null, null, "Drck1 aliquot", null, "isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult female gut", "Drck1", "Drck1", "Gene expression in zebrafish stimulated by heavy metals", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP199735", null, null, "Drck1 (pooling35-ACTTGA_HY2FYCCXY_L8_1.fq and pooling35-ACTTGA_HY2FYCCXY_L8_2.fq).gz", "fastq", 3523656300.0, 23491042.0, "Drck1 pooling35 ACTTGA HY2FYCCXY L8 1.fq and pooling35 ACTTGA HY2FYCCXY L8 2.fq.gz", "0:0 1:150", "A:973145926;C:804077269;G:862830763;T:883447878;N:154464", 0, 150, null, null, 973145926, 804077269, 862830763, 883447878, 154464, "SRX5914452", "SRS4832640", "SRA891446", "Kunming University of Science and Technology|College of Life Science", "Kunming University of Science and Technology", 1, 0.93236, null, 0.03761, null, 0.7134, null, 0.49667, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-29", "Adult", "Adult", "Gut", "Digestive System"], [52343, "SRR9141307", "SRX5914451", "SRS4832639", "SRP199735", "PRJNA545244", "Zebrafish transcriptome data", "PRJNA545244", "Other", "Heavy metals stimulate zebrafish", null, null, null, null, "Drck2 aliquot", null, "isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult female gut", "Drck2", "Drck2", "Gene expression in zebrafish stimulated by heavy metals", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP199735", null, null, "Drck2 (pooling35-GATCAG_HY2FYCCXY_L8_1.fq and pooling35-GATCAG_HY2FYCCXY_L8_2.fq).gz", "fastq", 3720733950.0, 24804893.0, "Drck2 pooling35 GATCAG HY2FYCCXY L8 1.fq and pooling35 GATCAG HY2FYCCXY L8 2.fq.gz", "0:0 1:150", "A:1041160797;C:830715515;G:904059203;T:944636106;N:162329", 0, 150, null, null, 1041160797, 830715515, 904059203, 944636106, 162329, "SRX5914451", "SRS4832639", "SRA891446", "Kunming University of Science and Technology|College of Life Science", "Kunming University of Science and Technology", 1, 0.91965, null, 0.0417, null, 0.70483, null, 0.48829, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-29", "Adult", "Adult", "Gut", "Digestive System"], [53020, "SRR9662019", "SRX6422895", "SRS5079685", "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 rep1", "GSM3934887", null, "source name:Tissue|strain:Tuebingen|tissue:Intestine", "YueLab RNA Seq Intestine rep1", "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", "GSM3934887", "GSM3934887: YueLab RNA Seq Intestine rep1; Danio rerio; RNA Seq", "GSM3934887", 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:GSM3934887", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Intestine-rep1_1.fastq.gz YueLab-RNA-Seq-Intestine-rep1_2.fastq.gz", "fastq fastq", 3793725541.0, 31407590.0, "GSM3934887 r1", "0:60.48 1:60.31", "A:996160866;C:872713802;G:866478996;T:1058315641;N:56236", 60, 60, null, null, 996160866, 872713802, 866478996, 1058315641, 56236, "SRX6422895", "SRS5079685", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.96494, 0.96816, 0.10241, 0.09966, 0.73705, 0.73992, 0.53336, 0.5394, 61, 61, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Gut", "Digestive System"], [55951, "SRR10827995", "SRX7501389", "SRS5942789", "SRP239446", "PRJNA598916", "Zebrafish intestinal gene expression", "PRJNA598916", "Other", "An analysis of zebrafish intestinal gene expression", null, null, null, null, "ZR011", null, "strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev stage:Adult|sex:male|tissue:whole intestine|replicate:replicate10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult 5D intestine", "ZR011", "ZR011", "Illumina Paired end sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP239446", null, null, "lane9-ZR011_S00_L009_R2_001.fastq.gz lane9-ZR011_S00_L009_R1_001.fastq.gz", "fastq fastq", 9665147298.0, 32003799.0, "lane9 ZR011 S00 L009 R1 001.fastq.gz", "0:151 1:151", "A:2665223251;C:2186863125;G:2211599706;T:2600518585;N:942631", 151, 151, null, null, 2665223251, 2186863125, 2211599706, 2600518585, 942631, "SRX7501389", "SRS5942789", "SRA1020118", "Oregon State University|Microbiology", "Oregon State University", 2, 0.85775, 0.85388, 0.06267, 0.06297, 0.78766, 0.79097, 0.54825, 0.54162, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-01-04", "Adult", "Adult", "Gut", "Digestive System"], [55952, "SRR10827996", "SRX7501388", "SRS5942788", "SRP239446", "PRJNA598916", "Zebrafish intestinal gene expression", "PRJNA598916", "Other", "An analysis of zebrafish intestinal gene expression", null, null, null, null, "ZR010", null, "strain:5D|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|dev 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