{"database": "metadata", "table": "run_metadata", "rows": [[63601, "SRR13951243", "SRX10330040", "SRS8449842", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype  akr1a1a /  and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level  we performed full genome RNA Seq between akr1a1a+/+  akr1a1a /  and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq  including quality control  principal component analysis PCA  and volcano plots of regulated genes showed comparable properties between akr1a1a mutants  wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score   1.888  p=0.028;  1.93  p=0.019. Intriguingly  downstream signaling pathways including MAPK  signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together  these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore  we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype  akr1a1a /   and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae akr1a1a KO rep3", "GSM5169476", null, "source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae akr1a1a KO rep3", "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.", "Zebrafish larvae akr1a1a KO larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "GSM5169476", "GSM5169476: Zebrafish larvae akr1a1a KO rep3; Danio rerio; RNA Seq", "GSM5169476", null, "1", "Larvae were collected  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169476", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAAORAAPEI-518_1.fq.gz V300079388_L3_HK500ZEBaopEAAORAAPEI-518_2.fq.gz", "fastq fastq", 4978639200.0, 49786392.0, "GSM5169476 r1", "0:100 1:100", "A:1331238273;C:1143633964;G:1152228372;T:1351538591;N:0", 100, 100, null, null, 1331238273, 1143633964, 1152228372, 1351538591, 0, "SRX10330040", "SRS8449842", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94616, null, 0.1007, null, 0.66054, null, 0.46712, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"]], "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": ["63601"], "units": {}, "query_ms": 8.266798002296127}