{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Juvenile\" and experiment.platform = \"BGISEQ\"", "rows": [[65887, "SRR15667963", "SRX11964789", "SRS9973857", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 6", "GSM5549117", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "liver  train overfeed 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "GSM5549117", "GSM5549117: liver  train overfeed 6; Danio rerio; RNA Seq", "GSM5549117", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L24B_1.fq.gz L24B_2.fq.gz", "fastq fastq", 4893222400.0, 48932224.0, "GSM5549117 r1", "0:100 1:100", "A:1299363606;C:1127714226;G:1149448002;T:1316696566;N:0", 100, 100, null, null, 1299363606, 1127714226, 1149448002, 1316696566, 0, "SRX11964789", "SRS9973857", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94811, null, 0.06102, null, 0.81306, null, 0.58353, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65888, "SRR15667962", "SRX11964788", "SRS9973856", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 5", "GSM5549116", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "liver  train overfeed 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "GSM5549116", "GSM5549116: liver  train overfeed 5; Danio rerio; RNA Seq", "GSM5549116", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L23B_1.fq.gz L23B_2.fq.gz", "fastq fastq", 4864315800.0, 48643158.0, "GSM5549116 r1", "0:100 1:100", "A:1269157216;C:1139579077;G:1173873653;T:1281705854;N:0", 100, 100, null, null, 1269157216, 1139579077, 1173873653, 1281705854, 0, "SRX11964788", "SRS9973856", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94747, null, 0.0487, null, 0.81779, null, 0.56304, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65889, "SRR15667961", "SRX11964787", "SRS9973855", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 4", "GSM5549115", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "liver  train overfeed 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "GSM5549115", "GSM5549115: liver  train overfeed 4; Danio rerio; RNA Seq", "GSM5549115", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L22B_1.fq.gz L22B_2.fq.gz", "fastq fastq", 4861767400.0, 48617674.0, "GSM5549115 r1", "0:100 1:100", "A:1272156595;C:1138672054;G:1163686667;T:1287252084;N:0", 100, 100, null, null, 1272156595, 1138672054, 1163686667, 1287252084, 0, "SRX11964787", "SRS9973855", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95316, null, 0.0514, null, 0.82008, null, 0.50642, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65890, "SRR15667960", "SRX11964786", "SRS9973854", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 3", "GSM5549114", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "liver  train overfeed 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "GSM5549114", "GSM5549114: liver  train overfeed 3; Danio rerio; RNA Seq", "GSM5549114", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L21B_1.fq.gz L21B_2.fq.gz", "fastq fastq", 4830571800.0, 48305718.0, "GSM5549114 r1", "0:100 1:100", "A:1279428022;C:1123545637;G:1144703564;T:1282894577;N:0", 100, 100, null, null, 1279428022, 1123545637, 1144703564, 1282894577, 0, "SRX11964786", "SRS9973854", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95734, null, 0.02001, null, 0.8868, null, 0.12725, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65891, "SRR15667959", "SRX11964785", "SRS9973853", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 2", "GSM5549113", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "liver  train overfeed 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "GSM5549113", "GSM5549113: liver  train overfeed 2; Danio rerio; RNA Seq", "GSM5549113", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L20B_1.fq.gz L20B_2.fq.gz", "fastq fastq", 4798900200.0, 47989002.0, "GSM5549113 r1", "0:100 1:100", "A:1264903507;C:1122454994;G:1142785530;T:1268756169;N:0", 100, 100, null, null, 1264903507, 1122454994, 1142785530, 1268756169, 0, "SRX11964785", "SRS9973853", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95953, null, 0.02579, null, 0.87251, null, 0.20039, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65892, "SRR15667958", "SRX11964784", "SRS9973852", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 1", "GSM5549112", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "liver  train overfeed 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "GSM5549112", "GSM5549112: liver  train overfeed 1; Danio rerio; RNA Seq", "GSM5549112", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L19B_1.fq.gz L19B_2.fq.gz", "fastq fastq", 4834397800.0, 48343978.0, "GSM5549112 r1", "0:100 1:100", "A:1279393804;C:1125815329;G:1148443590;T:1280745077;N:0", 100, 100, null, null, 1279393804, 1125815329, 1148443590, 1280745077, 0, "SRX11964784", "SRS9973852", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95933, null, 0.02008, null, 0.89483, null, 0.14592, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65893, "SRR15667957", "SRX11964783", "SRS9973851", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 6", "GSM5549111", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "liver  train ctrl 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "GSM5549111", "GSM5549111: liver  train ctrl 6; Danio rerio; RNA Seq", "GSM5549111", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L18B_1.fq.gz L18B_2.fq.gz", "fastq fastq", 4821948400.0, 48219484.0, "GSM5549111 r1", "0:100 1:100", "A:1291565962;C:1101325255;G:1121237816;T:1307819367;N:0", 100, 100, null, null, 1291565962, 1101325255, 1121237816, 1307819367, 0, "SRX11964783", "SRS9973851", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94729, null, 0.06306, null, 0.81207, null, 0.58228, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65894, "SRR15667956", "SRX11964782", "SRS9973850", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 5", "GSM5549110", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "liver  train ctrl 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "GSM5549110", "GSM5549110: liver  train ctrl 5; Danio rerio; RNA Seq", "GSM5549110", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L17B_1.fq.gz L17B_2.fq.gz", "fastq fastq", 4803628200.0, 48036282.0, "GSM5549110 r1", "0:100 1:100", "A:1284799467;C:1098135007;G:1120469212;T:1300224514;N:0", 100, 100, null, null, 1284799467, 1098135007, 1120469212, 1300224514, 0, "SRX11964782", "SRS9973850", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9496, null, 0.0625, null, 0.81456, null, 0.59107, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65895, "SRR15667955", "SRX11964781", "SRS9973849", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 4", "GSM5549109", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "liver  train ctrl 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "GSM5549109", "GSM5549109: liver  train ctrl 4; Danio rerio; RNA Seq", "GSM5549109", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L16B_1.fq.gz L16B_2.fq.gz", "fastq fastq", 4810847400.0, 48108474.0, "GSM5549109 r1", "0:100 1:100", "A:1282522728;C:1105003262;G:1127602301;T:1295719109;N:0", 100, 100, null, null, 1282522728, 1105003262, 1127602301, 1295719109, 0, "SRX11964781", "SRS9973849", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94654, null, 0.05935, null, 0.81525, null, 0.55406, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65896, "SRR15667954", "SRX11964780", "SRS9973848", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 3", "GSM5549108", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "liver  train ctrl 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "GSM5549108", "GSM5549108: liver  train ctrl 3; Danio rerio; RNA Seq", "GSM5549108", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L15B_1.fq.gz L15B_2.fq.gz", "fastq fastq", 4985037400.0, 49850374.0, "GSM5549108 r1", "0:100 1:100", "A:1350433123;C:1126555415;G:1149552334;T:1358496528;N:0", 100, 100, null, null, 1350433123, 1126555415, 1149552334, 1358496528, 0, "SRX11964780", "SRS9973848", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94223, null, 0.05241, null, 0.81753, null, 0.38734, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65897, "SRR15667953", "SRX11964779", "SRS9973847", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 2", "GSM5549107", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "liver  train ctrl 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "GSM5549107", "GSM5549107: liver  train ctrl 2; Danio rerio; RNA Seq", "GSM5549107", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L14B_1.fq.gz L14B_2.fq.gz", "fastq fastq", 4804454800.0, 48044548.0, "GSM5549107 r1", "0:100 1:100", "A:1265573746;C:1124189778;G:1148662079;T:1266029197;N:0", 100, 100, null, null, 1265573746, 1124189778, 1148662079, 1266029197, 0, "SRX11964779", "SRS9973847", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95891, null, 0.02268, null, 0.88392, null, 0.17772, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65898, "SRR15667952", "SRX11964778", "SRS9973846", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 1", "GSM5549106", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "liver  train ctrl 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "GSM5549106", "GSM5549106: liver  train ctrl 1; Danio rerio; RNA Seq", "GSM5549106", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L13B_1.fq.gz L13B_2.fq.gz", "fastq fastq", 4822830200.0, 48228302.0, "GSM5549106 r1", "0:100 1:100", "A:1276481281;C:1123835516;G:1144873235;T:1277640168;N:0", 100, 100, null, null, 1276481281, 1123835516, 1144873235, 1277640168, 0, "SRX11964778", "SRS9973846", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.96141, null, 0.0197, null, 0.89388, null, 0.1349, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65899, "SRR15667951", "SRX11964777", "SRS9973845", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 6", "GSM5549105", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "liver  ctrl overfeed 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "GSM5549105", "GSM5549105: liver  ctrl overfeed 6; Danio rerio; RNA Seq", "GSM5549105", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L9B_1.fq.gz L9B_2.fq.gz", "fastq fastq", 4818164600.0, 48181646.0, "GSM5549105 r1", "0:100 1:100", "A:1279585168;C:1117941633;G:1137085086;T:1283552713;N:0", 100, 100, null, null, 1279585168, 1117941633, 1137085086, 1283552713, 0, "SRX11964777", "SRS9973845", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95794, null, 0.0217, null, 0.8772, null, 0.13327, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65900, "SRR15667950", "SRX11964776", "SRS9973844", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 5", "GSM5549104", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "liver  ctrl overfeed 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "GSM5549104", "GSM5549104: liver  ctrl overfeed 5; Danio rerio; RNA Seq", "GSM5549104", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L8B_1.fq.gz L8B_2.fq.gz", "fastq fastq", 4815366200.0, 48153662.0, "GSM5549104 r1", "0:100 1:100", "A:1274920749;C:1122213902;G:1140211257;T:1278020292;N:0", 100, 100, null, null, 1274920749, 1122213902, 1140211257, 1278020292, 0, "SRX11964776", "SRS9973844", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95864, null, 0.02123, null, 0.88805, null, 0.13863, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65901, "SRR15667949", "SRX11964775", "SRS9973843", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 4", "GSM5549103", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "liver  ctrl overfeed 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "GSM5549103", "GSM5549103: liver  ctrl overfeed 4; Danio rerio; RNA Seq", "GSM5549103", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L7B_1.fq.gz L7B_2.fq.gz", "fastq fastq", 4806451200.0, 48064512.0, "GSM5549103 r1", "0:100 1:100", "A:1272428504;C:1119437887;G:1139899400;T:1274685409;N:0", 100, 100, null, null, 1272428504, 1119437887, 1139899400, 1274685409, 0, "SRX11964775", "SRS9973843", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9605, null, 0.02337, null, 0.87625, null, 0.17173, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65902, "SRR15667948", "SRX11964774", "SRS9973842", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 3", "GSM5549102", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "liver  ctrl overfeed 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "GSM5549102", "GSM5549102: liver  ctrl overfeed 3; Danio rerio; RNA Seq", "GSM5549102", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L12B_1.fq.gz L12B_2.fq.gz", "fastq fastq", 4808986200.0, 48089862.0, "GSM5549102 r1", "0:100 1:100", "A:1282711930;C:1106482446;G:1126540026;T:1293251798;N:0", 100, 100, null, null, 1282711930, 1106482446, 1126540026, 1293251798, 0, "SRX11964774", "SRS9973842", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95163, null, 0.05783, null, 0.80872, null, 0.56282, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65903, "SRR15667947", "SRX11964773", "SRS9973841", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 2", "GSM5549101", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "liver  ctrl overfeed 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "GSM5549101", "GSM5549101: liver  ctrl overfeed 2; Danio rerio; RNA Seq", "GSM5549101", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L11B_1.fq.gz L11B_2.fq.gz", "fastq fastq", 4813626000.0, 48136260.0, "GSM5549101 r1", "0:100 1:100", "A:1280868095;C:1108012462;G:1126540954;T:1298204489;N:0", 100, 100, null, null, 1280868095, 1108012462, 1126540954, 1298204489, 0, "SRX11964773", "SRS9973841", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94831, null, 0.05349, null, 0.81513, null, 0.57243, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65904, "SRR15667946", "SRX11964772", "SRS9973840", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 1", "GSM5549100", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "liver  ctrl overfeed 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "GSM5549100", "GSM5549100: liver  ctrl overfeed 1; Danio rerio; RNA Seq", "GSM5549100", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L10B_1.fq.gz L10B_2.fq.gz", "fastq fastq", 4810219200.0, 48102192.0, "GSM5549100 r1", "0:100 1:100", "A:1291986049;C:1097301072;G:1114733041;T:1306199038;N:0", 100, 100, null, null, 1291986049, 1097301072, 1114733041, 1306199038, 0, "SRX11964772", "SRS9973840", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9477, null, 0.06719, null, 0.80762, null, 0.56967, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65905, "SRR15667945", "SRX11964771", "SRS9973839", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 6", "GSM5549099", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "liver  ctrl ctrl 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "GSM5549099", "GSM5549099: liver  ctrl ctrl 6; Danio rerio; RNA Seq", "GSM5549099", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L6B_1.fq.gz L6B_2.fq.gz", "fastq fastq", 4800718000.0, 48007180.0, "GSM5549099 r1", "0:100 1:100", "A:1258342638;C:1122320482;G:1144931913;T:1275122967;N:0", 100, 100, null, null, 1258342638, 1122320482, 1144931913, 1275122967, 0, "SRX11964771", "SRS9973839", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.953, null, 0.05324, null, 0.81257, null, 0.58562, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65906, "SRR15667944", "SRX11964770", "SRS9973838", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 5", "GSM5549098", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "liver  ctrl ctrl 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "GSM5549098", "GSM5549098: liver  ctrl ctrl 5; Danio rerio; RNA Seq", "GSM5549098", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549098", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L5B_1.fq.gz L5B_2.fq.gz", "fastq fastq", 4806088800.0, 48060888.0, "GSM5549098 r1", "0:100 1:100", "A:1271888694;C:1114093824;G:1133421540;T:1286684742;N:0", 100, 100, null, null, 1271888694, 1114093824, 1133421540, 1286684742, 0, "SRX11964770", "SRS9973838", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95001, null, 0.05792, null, 0.807, null, 0.56126, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65907, "SRR15667943", "SRX11964769", "SRS9973837", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 4", "GSM5549097", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "liver  ctrl ctrl 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "GSM5549097", "GSM5549097: liver  ctrl ctrl 4; Danio rerio; RNA Seq", "GSM5549097", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549097", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L4B_1.fq.gz L4B_2.fq.gz", "fastq fastq", 4793658200.0, 47936582.0, "GSM5549097 r1", "0:100 1:100", "A:1278328591;C:1101882376;G:1120230481;T:1293216752;N:0", 100, 100, null, null, 1278328591, 1101882376, 1120230481, 1293216752, 0, "SRX11964769", "SRS9973837", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94635, null, 0.06821, null, 0.77814, null, 0.57203, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65908, "SRR15667942", "SRX11964768", "SRS9973836", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 3", "GSM5549096", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "liver  ctrl ctrl 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "GSM5549096", "GSM5549096: liver  ctrl ctrl 3; Danio rerio; RNA Seq", "GSM5549096", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549096", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L3B_1.fq.gz L3B_2.fq.gz", "fastq fastq", 4826663000.0, 48266630.0, "GSM5549096 r1", "0:100 1:100", "A:1279595092;C:1123953174;G:1141367365;T:1281747369;N:0", 100, 100, null, null, 1279595092, 1123953174, 1141367365, 1281747369, 0, "SRX11964768", "SRS9973836", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9594, null, 0.02127, null, 0.88463, null, 0.12493, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65909, "SRR15667941", "SRX11964767", "SRS9973835", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 2", "GSM5549095", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "liver  ctrl ctrl 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "GSM5549095", "GSM5549095: liver  ctrl ctrl 2; Danio rerio; RNA Seq", "GSM5549095", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549095", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L2B_1.fq.gz L2B_2.fq.gz", "fastq fastq", 4825604600.0, 48256046.0, "GSM5549095 r1", "0:100 1:100", "A:1280321186;C:1120511740;G:1138899889;T:1285871785;N:0", 100, 100, null, null, 1280321186, 1120511740, 1138899889, 1285871785, 0, "SRX11964767", "SRS9973835", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95896, null, 0.0192, null, 0.88899, null, 0.11515, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65910, "SRR15667940", "SRX11964766", "SRS9973834", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 1", "GSM5549094", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "liver  ctrl ctrl 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "GSM5549094", "GSM5549094: liver  ctrl ctrl 1; Danio rerio; RNA Seq", "GSM5549094", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549094", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L1B_1.fq.gz L1B_2.fq.gz", "fastq fastq", 4829756800.0, 48297568.0, "GSM5549094 r1", "0:100 1:100", "A:1282017434;C:1119791375;G:1138880812;T:1289067179;N:0", 100, 100, null, null, 1282017434, 1119791375, 1138880812, 1289067179, 0, "SRX11964766", "SRS9973834", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95838, null, 0.03146, null, 0.8479, null, 0.28451, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [68196, "SRR17658725", "SRX13826756", "SRS11705914", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "T60d  ZHT", null, "strain:AB|isolate:35|breed:zebrafish|cultivar:TEST|ecotype:CHINA|age:60dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "T60D", "T60D", "heat treated zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20334742200.0, 67782474.0, "T60D.7z", "0:150 1:150", "A:5482201207;C:4682998764;G:4635775004;T:5533378494;N:388731", 150, 150, null, null, 5482201207, 4682998764, 4635775004, 5533378494, 388731, "SRX13826756", "SRS11705914", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.94378, 0.94515, 0.04989, 0.04997, 0.69848, 0.69978, 0.50317, 0.5041, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68197, "SRR17658726", "SRX13826755", "SRS11705913", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "T45d  ZHT", null, "strain:AB|isolate:35|breed:zebrafish|cultivar:TEST|ecotype:CHINA|age:45dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "T45D", "T45D", "heat treated zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20230560300.0, 67435201.0, "T45D.7z", "0:150 1:150", "A:5444816209;C:4663007584;G:4631943733;T:5490408754;N:384020", 150, 150, null, null, 5444816209, 4663007584, 4631943733, 5490408754, 384020, "SRX13826755", "SRS11705913", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.88041, 0.881, 0.04485, 0.04492, 0.72163, 0.72236, 0.52232, 0.52307, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68198, "SRR17658727", "SRX13826754", "SRS11705912", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "T35d  ZHT", null, "strain:AB|isolate:35|breed:zebrafish|cultivar:TEST|ecotype:CHINA|age:35dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "T35D", "T35D", "heat treated zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20630503200.0, 68768344.0, "T35D.7z", "0:150 1:150", "A:5660657832;C:4654929757;G:4598083304;T:5716350276;N:482031", 150, 150, null, null, 5660657832, 4654929757, 4598083304, 5716350276, 482031, "SRX13826754", "SRS11705912", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.9134, 0.91476, 0.06961, 0.06972, 0.69035, 0.69215, 0.52155, 0.5154, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68199, "SRR17658728", "SRX13826753", "SRS11705911", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C60d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:60dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C60D", "C60D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 10921407600.0, 44923977.0, "C60D.7z", null, "A:2992232295;C:2470688717;G:2440861228;T:3017432565;N:192795", null, null, null, null, 2992232295, 2470688717, 2440861228, 3017432565, 192795, "SRX13826753", "SRS11705911", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.93932, 0.94095, 0.06489, 0.06559, 0.77871, 0.77759, 0.56384, 0.56447, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68200, "SRR17658729", "SRX13826752", "SRS11705910", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C45d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:45dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C45D", "C45D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20413229700.0, 68044099.0, "C45D.7z", "0:150 1:150", "A:5619395833;C:4581611789;G:4543973618;T:5667873613;N:374847", 150, 150, null, null, 5619395833, 4581611789, 4543973618, 5667873613, 374847, "SRX13826752", "SRS11705910", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.86848, 0.87064, 0.0719, 0.07252, 0.69879, 0.69834, 0.52279, 0.51074, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68201, "SRR17658730", "SRX13826751", "SRS11705909", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C35d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:35dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C35D", "C35D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20469803700.0, 68232679.0, "C35D.7z", "0:150 1:150", "A:5556774511;C:4678377106;G:4627472920;T:5606765895;N:413268", 150, 150, null, null, 5556774511, 4678377106, 4627472920, 5606765895, 413268, "SRX13826751", "SRS11705909", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.93663, 0.93871, 0.06853, 0.06895, 0.6982, 0.69901, 0.51209, 0.51148, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69610, "SRR18959644", "SRX15036823", "SRS12783659", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 3", "GSM6070558", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070558", "GSM6070558: T60d 3; Danio rerio; RNA Seq", "GSM6070558 r1", "GSM6070558", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_3_1.fq.gz T60d_3_2.fq.gz", "fastq fastq", 6668586300.0, 44457242.0, "GSM6070558 r1", "0:150 1:150", "A:1798105768;C:1533776293;G:1519933345;T:1816635529;N:135365", 150, 150, null, null, 1798105768, 1533776293, 1519933345, 1816635529, 135365, "SRX15036823", "SRS12783659", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94696, null, 0.03818, null, 0.72754, null, 0.44424, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69611, "SRR18959645", "SRX15036822", "SRS12783660", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 2", "GSM6070557", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070557", "GSM6070557: T60d 2; Danio rerio; RNA Seq", "GSM6070557 r1", "GSM6070557", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_2_1.fq.gz T60d_2_2.fq.gz", "fastq fastq", 6790474800.0, 45269832.0, "GSM6070557 r1", "0:150 1:150", "A:1792022273;C:1601949824;G:1583360851;T:1813022005;N:119847", 150, 150, null, null, 1792022273, 1601949824, 1583360851, 1813022005, 119847, "SRX15036822", "SRS12783660", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9518, null, 0.03662, null, 0.72892, null, 0.50564, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69612, "SRR18959646", "SRX15036821", "SRS12783661", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 1", "GSM6070556", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070556", "GSM6070556: T60d 1; Danio rerio; RNA Seq", "GSM6070556 r1", "GSM6070556", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_1_1.fq.gz T60d_1_2.fq.gz", "fastq fastq", 6875681100.0, 45837874.0, "GSM6070556 r1", "0:150 1:150", "A:1892073166;C:1547272647;G:1532480808;T:1903720960;N:133519", 150, 150, null, null, 1892073166, 1547272647, 1532480808, 1903720960, 133519, "SRX15036821", "SRS12783661", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93516, null, 0.0737, null, 0.70394, null, 0.55661, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69613, "SRR18959647", "SRX15036820", "SRS12783658", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 3", "GSM6070555", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070555", "GSM6070555: T45d 3; Danio rerio; RNA Seq", "GSM6070555 r1", "GSM6070555", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_3_1.fq.gz T45d_3_2.fq.gz", "fastq fastq", 6677602800.0, 44517352.0, "GSM6070555 r1", "0:150 1:150", "A:1776927020;C:1564627916;G:1551750199;T:1784113081;N:184584", 150, 150, null, null, 1776927020, 1564627916, 1551750199, 1784113081, 184584, "SRX15036820", "SRS12783658", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.95333, null, 0.04626, null, 0.79788, null, 0.53869, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69614, "SRR18959648", "SRX15036819", "SRS12783657", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 2", "GSM6070554", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070554", "GSM6070554: T45d 2; Danio rerio; RNA Seq", "GSM6070554 r1", "GSM6070554", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_2_1.fq.gz T45d_2_2.fq.gz", "fastq fastq", 6866885100.0, 45779234.0, "GSM6070554 r1", "0:150 1:150", "A:1855996561;C:1572989256;G:1559095064;T:1878636946;N:167273", 150, 150, null, null, 1855996561, 1572989256, 1559095064, 1878636946, 167273, "SRX15036819", "SRS12783657", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.85691, null, 0.0428, null, 0.70059, null, 0.48517, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69615, "SRR18959649", "SRX15036818", "SRS12783655", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 1", "GSM6070553", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070553", "GSM6070553: T45d 1; Danio rerio; RNA Seq", "GSM6070553 r1", "GSM6070553", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_1_1.fq.gz T45d_1_2.fq.gz", "fastq fastq", 6686072400.0, 44573816.0, "GSM6070553 r1", "0:150 1:150", "A:1811892628;C:1525390412;G:1521098470;T:1827658727;N:32163", 150, 150, null, null, 1811892628, 1525390412, 1521098470, 1827658727, 32163, "SRX15036818", "SRS12783655", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.83063, null, 0.04482, null, 0.75227, null, 0.53268, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69616, "SRR18959650", "SRX15036817", "SRS12783656", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 3", "GSM6070552", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070552", "GSM6070552: T35d 3; Danio rerio; RNA Seq", "GSM6070552 r1", "GSM6070552", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_3_1.fq.gz T35d_3_2.fq.gz", "fastq fastq", 6886247700.0, 45908318.0, "GSM6070552 r1", "0:150 1:150", "A:1822190170;C:1616493163;G:1597658988;T:1849741504;N:163875", 150, 150, null, null, 1822190170, 1616493163, 1597658988, 1849741504, 163875, "SRX15036817", "SRS12783656", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94299, null, 0.03719, null, 0.71165, null, 0.49413, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69617, "SRR18959651", "SRX15036816", "SRS12783654", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 2", "GSM6070551", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070551", "GSM6070551: T35d 2; Danio rerio; RNA Seq", "GSM6070551 r1", "GSM6070551", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_2_1.fq.gz T35d_2_2.fq.gz", "fastq fastq", 6851241900.0, 45674946.0, "GSM6070551 r1", "0:150 1:150", "A:1925245234;C:1503184374;G:1483632128;T:1939009289;N:170875", 150, 150, null, null, 1925245234, 1503184374, 1483632128, 1939009289, 170875, "SRX15036816", "SRS12783654", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.86703, null, 0.08277, null, 0.70619, null, 0.47871, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69618, "SRR18959652", "SRX15036815", "SRS12783653", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 1", "GSM6070550", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070550", "GSM6070550: T35d 1; Danio rerio; RNA Seq", "GSM6070550 r1", "GSM6070550", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_1_1.fq.gz T35d_1_2.fq.gz", "fastq fastq", 6893013600.0, 45953424.0, "GSM6070550 r1", "0:150 1:150", "A:1913222428;C:1535252220;G:1516792188;T:1927599483;N:147281", 150, 150, null, null, 1913222428, 1535252220, 1516792188, 1927599483, 147281, "SRX15036815", "SRS12783653", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93126, null, 0.08861, null, 0.70711, null, 0.53182, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69619, "SRR18959653", "SRX15036814", "SRS12783652", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 3", "GSM6070549", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070549", "GSM6070549: C60d 3; Danio rerio; RNA Seq", "GSM6070549 r1", "GSM6070549", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_3_1.fq.gz C60d_3_2.fq.gz", "fastq fastq", 6732458700.0, 44883058.0, "GSM6070549 r1", "0:150 1:150", "A:1840891044;C:1527037740;G:1515664962;T:1848770869;N:94085", 150, 150, null, null, 1840891044, 1527037740, 1515664962, 1848770869, 94085, "SRX15036814", "SRS12783652", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94478, null, 0.05996, null, 0.73661, null, 0.56885, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69620, "SRR18959654", "SRX15036813", "SRS12783651", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 2", "GSM6070548", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070548", "GSM6070548: C60d 2; Danio rerio; RNA Seq", "GSM6070548 r1", "GSM6070548", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_2_1.fq.gz C60d_2_2.fq.gz", "fastq fastq", 6920478600.0, 46136524.0, "GSM6070548 r1", "0:150 1:150", "A:1860288879;C:1602876302;G:1589399217;T:1867783032;N:131170", 150, 150, null, null, 1860288879, 1602876302, 1589399217, 1867783032, 131170, "SRX15036813", "SRS12783651", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.95235, null, 0.05236, null, 0.74836, null, 0.55427, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69621, "SRR18959655", "SRX15036812", "SRS12783650", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 1", "GSM6070547", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070547", "GSM6070547: C60d 1; Danio rerio; RNA Seq", "GSM6070547 r1", "GSM6070547", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_1_1.fq.gz C60d_1_2.fq.gz", "fastq fastq", 6744639300.0, 44964262.0, "GSM6070547 r1", "0:150 1:150", "A:1855599360;C:1516548729;G:1501772747;T:1870587619;N:130845", 150, 150, null, null, 1855599360, 1516548729, 1501772747, 1870587619, 130845, "SRX15036812", "SRS12783650", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93949, null, 0.06857, null, 0.73805, null, 0.54443, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69622, "SRR18959656", "SRX15036811", "SRS12783649", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 3", "GSM6070546", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070546", "GSM6070546: C45d 3; Danio rerio; RNA Seq", "GSM6070546 r1", "GSM6070546", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_3_1.fq.gz C45d_3_2.fq.gz", "fastq fastq", 6743568300.0, 44957122.0, "GSM6070546 r1", "0:150 1:150", "A:1852733188;C:1516814321;G:1505754587;T:1868137549;N:128655", 150, 150, null, null, 1852733188, 1516814321, 1505754587, 1868137549, 128655, "SRX15036811", "SRS12783649", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.87046, null, 0.07264, null, 0.69996, null, 0.51275, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69623, "SRR18959657", "SRX15036810", "SRS12783648", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 2", "GSM6070545", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070545", "GSM6070545: C45d 2; Danio rerio; RNA Seq", "GSM6070545 r1", "GSM6070545", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_2_1.fq.gz C45d_2_2.fq.gz", "fastq fastq", 6742016100.0, 44946774.0, "GSM6070545 r1", "0:150 1:150", "A:1859613225;C:1508260261;G:1496299109;T:1877718155;N:125350", 150, 150, null, null, 1859613225, 1508260261, 1496299109, 1877718155, 125350, "SRX15036810", "SRS12783648", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.84381, null, 0.07253, null, 0.68769, null, 0.51224, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69624, "SRR18959658", "SRX15036809", "SRS12783647", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 1", "GSM6070544", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070544", "GSM6070544: C45d 1; Danio rerio; RNA Seq", "GSM6070544 r1", "GSM6070544", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_1_1.fq.gz C45d_1_2.fq.gz", "fastq fastq", 6927645300.0, 46184302.0, "GSM6070544 r1", "0:150 1:150", "A:1907049420;C:1556537207;G:1541919922;T:1922017909;N:120842", 150, 150, null, null, 1907049420, 1556537207, 1541919922, 1922017909, 120842, "SRX15036809", "SRS12783647", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.89529, null, 0.07244, null, 0.71703, null, 0.53737, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69625, "SRR18959659", "SRX15036808", "SRS12783646", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 3", "GSM6070543", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070543", "GSM6070543: C35d 3; Danio rerio; RNA Seq", "GSM6070543 r1", "GSM6070543", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_3_1.fq.gz C35d_3_2.fq.gz", "fastq fastq", 6874832400.0, 45832216.0, "GSM6070543 r1", "0:150 1:150", "A:1849406781;C:1586828671;G:1570455371;T:1867999362;N:142215", 150, 150, null, null, 1849406781, 1586828671, 1570455371, 1867999362, 142215, "SRX15036808", "SRS12783646", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94372, null, 0.06412, null, 0.71043, null, 0.5035, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69626, "SRR18959660", "SRX15036807", "SRS12783645", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 2", "GSM6070542", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070542", "GSM6070542: C35d 2; Danio rerio; RNA Seq", "GSM6070542 r1", "GSM6070542", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_2_1.fq.gz C35d_2_2.fq.gz", "fastq fastq", 6709504200.0, 44730028.0, "GSM6070542 r1", "0:150 1:150", "A:1832012065;C:1521825928;G:1505192413;T:1850347840;N:125954", 150, 150, null, null, 1832012065, 1521825928, 1505192413, 1850347840, 125954, "SRX15036807", "SRS12783645", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9254, null, 0.07577, null, 0.67537, null, 0.51805, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69627, "SRR18959661", "SRX15036806", "SRS12783644", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 1", "GSM6070541", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070541", "GSM6070541: C35d 1; Danio rerio; RNA Seq", "GSM6070541 r1", "GSM6070541", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_1_1.fq.gz C35d_1_2.fq.gz", "fastq fastq", 6885467100.0, 45903114.0, "GSM6070541 r1", "0:150 1:150", "A:1875355665;C:1569722507;G:1551825136;T:1888418693;N:145099", 150, 150, null, null, 1875355665, 1569722507, 1551825136, 1888418693, 145099, "SRX15036806", "SRS12783644", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9444, null, 0.06579, null, 0.73312, null, 0.53564, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [76452, "SRR24950188", "SRX20708357", "SRS18001302", "SRP444408", "PRJNA984676", "RNA Seq analyses of myocardium specific hey2  overexpressing zebrafish hearts and Adv Hey2 infected NRVMs", "PRJNA984676", "Other", "To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction  we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria  we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.", null, null, null, "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  rep1", "OE1w1", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE1w replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  rep1", "OE1w replicate 1", "OE1w replicate 1", "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  replicate 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP444408", null, null, "OE1w1_1.fq.gz OE1w1_2.fq.gz", "fastq fastq", 6792141900.0, 22640473.0, "OE1w1 1.fq.gz", "0:150 1:150", "A:1821318465;C:1573309073;G:1556399365;T:1841095017;N:19980", 150, 150, null, null, 1821318465, 1573309073, 1556399365, 1841095017, 19980, "SRX20708357", "SRS18001302", "SRA1657339", "East China Normal University|School of Life Sciences", "East China Normal University", 2, 0.92576, 0.91367, 0.07095, 0.07022, 0.74884, 0.75012, 0.52564, 0.52623, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-06-16", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [76453, "SRR24950189", "SRX20708356", "SRS18001301", "SRP444408", "PRJNA984676", "RNA Seq analyses of myocardium specific hey2  overexpressing zebrafish hearts and Adv Hey2 infected NRVMs", "PRJNA984676", "Other", "To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction  we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria  we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.", null, null, null, "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  rep3", "CTL1w3", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL1w replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  rep3", "CTL1w replicate 3", "CTL1w replicate 3", "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  replicate 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP444408", null, null, "CTL1w3_2.fq.gz CTL1w3_1.fq.gz", "fastq fastq", 6615956700.0, 22053189.0, "CTL1w3 1.fq.gz", "0:150 1:150", "A:1790825663;C:1516487260;G:1497904437;T:1810720169;N:19171", 150, 150, null, null, 1790825663, 1516487260, 1497904437, 1810720169, 19171, "SRX20708356", "SRS18001301", "SRA1657339", "East China Normal University|School of Life Sciences", "East China Normal University", 2, 0.93183, 0.91562, 0.07118, 0.07012, 0.7655, 0.7682, 0.53912, 0.52899, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-06-16", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [76454, "SRR24950190", "SRX20708355", "SRS18001300", "SRP444408", "PRJNA984676", "RNA Seq analyses of myocardium specific hey2  overexpressing zebrafish hearts and Adv Hey2 infected NRVMs", "PRJNA984676", "Other", "To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction  we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria  we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.", null, null, null, "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  rep2", "CTL1w2", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL1w replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  rep2", "CTL1w replicate 2", "CTL1w replicate 2", "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  replicate 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP444408", null, null, "CTL1w2_1.fq.gz CTL1w2_2.fq.gz", "fastq fastq", 6582133800.0, 21940446.0, "CTL1w2 1.fq.gz", "0:150 1:150", "A:1766322301;C:1524014072;G:1506429130;T:1785350030;N:18267", 150, 150, null, null, 1766322301, 1524014072, 1506429130, 1785350030, 18267, "SRX20708355", "SRS18001300", "SRA1657339", "East China Normal University|School of Life Sciences", "East China Normal University", 2, 0.93867, 0.92389, 0.06545, 0.06458, 0.76357, 0.76583, 0.53821, 0.54255, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-06-16", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [76455, "SRR24950191", "SRX20708354", "SRS18001299", "SRP444408", "PRJNA984676", "RNA Seq analyses of myocardium specific hey2  overexpressing zebrafish hearts and Adv Hey2 infected NRVMs", "PRJNA984676", "Other", "To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction  we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria  we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.", null, null, null, "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  rep1", "CTL1w1", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL1w replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  rep1", "CTL1w replicate 1", "CTL1w replicate 1", "RNA Seq for control littermate hearts at 1 week post 4 HT treatments  replicate 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP444408", null, null, "CTL1w1_2.fq.gz CTL1w1_1.fq.gz", "fastq fastq", 6781172100.0, 22603907.0, "CTL1w1 1.fq.gz", "0:150 1:150", "A:1804085074;C:1581571692;G:1567430366;T:1828066356;N:18612", 150, 150, null, null, 1804085074, 1581571692, 1567430366, 1828066356, 18612, "SRX20708354", "SRS18001299", "SRA1657339", "East China Normal University|School of Life Sciences", "East China Normal University", 2, 0.93867, 0.91921, 0.06237, 0.06146, 0.75858, 0.76246, 0.53972, 0.53069, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-06-16", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [76460, "SRR24950198", "SRX20708347", "SRS18001292", "SRP444408", "PRJNA984676", "RNA Seq analyses of myocardium specific hey2  overexpressing zebrafish hearts and Adv Hey2 infected NRVMs", "PRJNA984676", "Other", "To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction  we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria  we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.", null, null, null, "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  rep3", "OE1w3", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE1w replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  rep3", "OE1w replicate 3", "OE1w replicate 3", "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  replicate 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP444408", null, null, "OE1w3_2.fq.gz OE1w3_1.fq.gz", "fastq fastq", 6593130600.0, 21977102.0, "OE1w3 1.fq.gz", "0:150 1:150", "A:1770061078;C:1529682678;G:1510949508;T:1782338558;N:98778", 150, 150, null, null, 1770061078, 1529682678, 1510949508, 1782338558, 98778, "SRX20708347", "SRS18001292", "SRA1657339", "East China Normal University|School of Life Sciences", "East China Normal University", 2, 0.93503, 0.922, 0.06588, 0.06574, 0.7503, 0.75201, 0.52969, 0.53743, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-06-16", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [76461, "SRR24950199", "SRX20708346", "SRS18001291", "SRP444408", "PRJNA984676", "RNA Seq analyses of myocardium specific hey2  overexpressing zebrafish hearts and Adv Hey2 infected NRVMs", "PRJNA984676", "Other", "To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction  we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria  we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.", null, null, null, "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  rep2", "OE1w2", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE1w replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  rep2", "OE1w replicate 2", "OE1w replicate 2", "RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments  replicate 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP444408", null, null, "OE1w2_2.fq.gz OE1w2_1.fq.gz", "fastq fastq", 6742724700.0, 22475749.0, "OE1w2 1.fq.gz", "0:150 1:150", "A:1802906309;C:1568304698;G:1553625077;T:1817795677;N:92939", 150, 150, null, null, 1802906309, 1568304698, 1553625077, 1817795677, 92939, "SRX20708346", "SRS18001291", "SRA1657339", "East China Normal University|School of Life Sciences", "East China Normal University", 2, 0.93354, 0.91844, 0.06989, 0.0686, 0.74665, 0.74888, 0.52723, 0.52812, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-06-16", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"]], "truncated": false, "filtered_table_rows_count": 54, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Juvenile", "p1": "BGISEQ"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", 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"type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ", "results": [{"value": "BGISEQ", "label": "BGISEQ", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Juvenile", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ", "results": [{"value": "Juvenile", "label": "Juvenile", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ&devstage_curation_coarse=Juvenile", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ", "results": [{"value": "Juvenile", "label": "Juvenile", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=BGISEQ", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Juvenile&experiment.platform=BGISEQ", "results": [{"value": "All anatomical 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