run_metadata: 31941

This data as json

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
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.		pubmed:38771396		WT Sibling Control 2	GSM8225395		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’ 3’ 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		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°C	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP503694		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			2377620319	2148477327	2213637714	2333593535	128805	SRX24351566	SRS21110448	SRA1851694	???	医学院												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Unknown	2024-04-23	Larval	Larval	Undetermined	Undetermined