{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "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": ["69623"], "units": {}, "query_ms": 13.477733009494841}