{"database": "metadata", "table": "run_metadata", "rows": [[31941, "SRR28787284", "SRX24351566", "SRS21110448", "SRP503694", "PRJNA1103784", "Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish", "GSE264674", "Transcriptome Analysis", "Purinergic receptor P2Y11  a G protein coupled receptor that is stimulated by the endogenous ATP  has been demonstrated to be related with the chemotaxis of granulocytes  apoptosis of neutrophils  and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However  little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study  we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function  we performed GO term analysis of the up regulated and down regulated DE genes of P2RY11 8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex GO:0098802  calcium ion binding GO:0005509  and protein refolding GO:0042026 were most enriched terms in up regulated DE genes. While metabolic process GO:008152  location Go:0051179 and cellular process GO:009987 were most enriched terms in down regulated DE genes . In addition  immune system process GO:0002376 was also enriched in down regulated DE genes of P2RY11 8bp versus WT controls . Basic on the genes related with immune system process  we further performed GO term enrichment analysis and found that the defense response  leukocyte chemiotaxis  and inflammatory response were the main enriched terms. Overall design: The p2ry11 /  mutant and  wild type WT sibling were produced from p2ry11 heterozygous +/  intercross embryos. Subsequently  RNA was extracted from the p2ry11 /  mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA seq of the mutant and WT siblings.", null, "pubmed:38771396", null, "WT Sibling Control 2", "GSM8225395", null, "source name:zebrafish larvae|tissue:zebrafish larvae|time:3 dpf loc name:missing|collection date:missing", "WT Sibling Control 2", "Image analysis and base calling were performed using Solexa pipeline v1.8 Off Line Base Caller software  v1.8 Sequence quality was examined using the FastQC softwarev0.11.7 The trimmed reads trimmed 5\u2019  3\u2019 adaptor bases using cutadaptv1.17 were aligned to reference genomeGRCh37 using Hisat2 softwarev2.1.0 The transcript abundance for each sample was estimated with StringTiev1.3.3  and the FPKM value for gene and transcript level was calculated with R package Ballgownv2.10.0 Assembly: GRCh37 Supplementary files format and content: the FPKM value of detected mRNA for each sample", "zebrafish larvae", null, "RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", "Larvae were kept in E3 medium with methylene blue at 28.5\u00b0C", "tissue:zebrafish larvae|time:3 dpf", "GSM8225395", "GSM8225395: WT Sibling Control 2; Danio rerio; RNA Seq", "GSM8225395 r1", "GSM8225395", "1", "RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503694", null, "loader:fastq load.py", "WT2_R1.fastq.gz WT2_R2.fastq.gz", "fastq fastq", 9073457700.0, 30244859.0, "GSM8225395 r1", "0:150 1:150", "A:2377620319;C:2148477327;G:2213637714;T:2333593535;N:128805", 150, 150, null, null, 2377620319, 2148477327, 2213637714, 2333593535, 128805, "SRX24351566", "SRS21110448", "SRA1851694", "???", "\u533b\u5b66\u9662", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-04-23", "Larval", "Larval", "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": ["31941"], "units": {}, "query_ms": 6.037826000465429}