run_metadata: 50716

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
50716	SRR8255919	SRX5073699	SRS4087525	SRP171016	PRJNA507363	Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection	GSE123036	Transcriptome Analysis	To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.		pubmed:30679186		Con rep1	GSM3494231		source name:Pancreatic beta cells\|genotype/variation:Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:wild type	Con rep1	Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Pancreatic beta cells		Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype/variation:Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:wild type	GSM3494231	GSM3494231: Con rep1; Danio rerio; RNA Seq	GSM3494231		1	Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3494231	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP171016			L19372_Track-47628_R1.fastq.gz	fastq	3743010792.0	49250142.0	GSM3494231 r1	0:76	A:1081119100;C:816543927;G:821868656;T:1023236057;N:243052	76				1081119100	816543927	821868656	1023236057	243052	SRX5073699	SRS4087525	SRA815642	GEO	Ninov, CRTD	1	0.87612		0.16984		0.7684		0.57882		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Germany	2018-11-28	Adult	Adult	Pancreas	Endocrine System