{"database": "metadata", "table": "run_metadata", "rows": [[63877, "SRR14163086", "SRX10531556", "SRS8654917", "SRP313793", "PRJNA720320", "Quantitative Analysis of Transcriptomes of Control and BP 3 exposure embryos zebrafish by RNA sequencing", "GSE171619", "Transcriptome Analysis", "Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without xxx 3BP 3 at the transcriptome level and find the underlying mechanism how could BP 3 impede the development of enteric nervous system. Methods:  Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos were generated by paired end sequencing  in triplicate  using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis GSEA comparing WT and BP 3 exposure groups was performed by GSEA software version 4.0.03. A nominal p value < 0.05 and false discovery rate FDR q value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. RNA seq data confirmed 159 up regulated and 73 down regulated genes in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP 3 exposure zebrafish intestinal transcriptomes  with biologic replicates  generated by RNA sequencing technology. Our results showed that 159 genes were up regulated and 73 were down regulated  in BP 3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Overall design: Intestinal RNA profiles of 5dpf Wide Type WT and BP 3 exposure groups of zebrafish embryos", null, null, null, "WT 1", "GSM5229429", null, "source name:Intestinal|strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control", "WT 1", "Illumina HiSeqTM 2500 used for basecalling. specific steps were followed using the methods previously described WEI L  CAO L  MIAO Y  et al. Transcriptome analysis of Spodoptera frugiperda 9 Sf9 cells infected with baculovirus  AcMNPV or AcMNPV BmK IT [J]. Biotechnol Lett  2017  398: 1129 39. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 FoldChange| > 1 & qvalue<0.05 as the DEGs. Genome build: mm9 Supplementary files format and content: tab delimited text files include MEAN TPM values for each Sample", "Intestinal", "Embryos of BP 3 exposure group were incubated in 2mg/L BP 3", "intestinal tissues of embryos were dissected by microforceps. All samples were stored at \u221280\u00b0C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer\u2019s instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:zebrafish|tissue:intestinal|age:5dpf|treatment:Control", "GSM5229429", "GSM5229429: WT 1; Danio rerio; RNA Seq", "GSM5229429", null, "1", "intestinal tissues of embryos were dissected by microforceps. All samples were stored at \u221280\u00b0C until total RNA extraction. Total RNA extraction was performed with TRIZol reagents from Invitrogen following the manufacturer's instructions. cDNA libraries were constructed and adopted the paired end sequencing on an Illumina HiSeqTM 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5229429", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP313793", null, "loader:fastq load.py", "WT_1.raw_1.fastq.gz", "fastq", 4168065900.0, 27787106.0, "GSM5229429 r1", "0:150", "A:1120621692;C:971245010;G:991822128;T:1084366148;N:10922", 150, null, null, null, 1120621692, 971245010, 991822128, 1084366148, 10922, "SRX10531556", "SRS8654917", "SRA1215917", "GEO", "Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology", 1, 0.95088, null, 0.10223, null, 0.64932, null, 0.47628, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-04-07", "Larval", "Larval", "Gut", "Digestive 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": ["63877"], "units": {}, "query_ms": 10.359009000239894}