run_metadata: 59159

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
59159	SRR11700440	SRX8259895	SRS6601863	SRP260213	PRJNA630667	RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae	GSE149942	Transcriptome Analysis	The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal lysosomal and Golgi related genes were most frequently up regulated. Moreover lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note several lysosomal markers including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 / and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech prior Illumina sequencing.		pubmed:33852860		cxcr3.2mu rep1	GSM4518493		tissue:FACS mpeg1: mCherryF positive cells\|age:6 dpf type:macrophage\|strain:mpeg1: mCherryF\|genotype:cxcr3.2 /	cxcr3.2mu rep1	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample	FACS mpeg1: mCherryF positive cells		3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 / and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.		age:6 dpf type:macrophage\|strain:mpeg1: mCherryF\|genotype:cxcr3.2 /	GSM4518493	GSM4518493: cxcr3.2mu rep1; Danio rerio; RNA Seq	GSM4518493		1	3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 / and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.	GEO Accession:GSM4518493	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP260213			mu1_2.fastq.gz	fastq	417048216.0	8177416.0	GSM4518493 r2	0:51	A:119015831;C:83862032;G:84384304;T:129702704;N:83345	51				119015831	83862032	84384304	129702704	83345	SRX8259895	SRS6601863	SRA1072497	GEO	LSHTM	1	0.74816		0.18628		0.78782		0.52889		51		B		usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown		United Kingdom	2020-05-06	Larval	Larval	Blood	Hematopoietic System