{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "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": ["rowid"], "primary_key_values": ["65898"], "units": {}, "query_ms": 10.47436199587537}