{"database": "metadata", "table": "run_metadata", "rows": [[50713, "SRR8255922", "SRX5073702", "SRS4087528", "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.", null, "pubmed:30679186", null, "Il1B rep2", "GSM3494234", null, "source name:Pancreatic beta cells|genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells", "Il1B rep2", "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", null, "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\u02daC 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\u02daC. 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", null, "genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells", "GSM3494234", "GSM3494234: Il1B rep2; Danio rerio; RNA Seq", "GSM3494234", null, "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\u02daC 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\u02daC. 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:GSM3494234", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP171016", null, null, "L19371_Track-47496_R1.fastq.gz", "fastq", 3282305632.0, 43188232.0, "GSM3494234 r1", "0:76 1:0", "A:961171458;C:699797228;G:707162172;T:914140351;N:34423", 76, 0, null, null, 961171458, 699797228, 707162172, 914140351, 34423, "SRX5073702", "SRS4087528", "SRA815642", "GEO", "Ninov, CRTD", 1, 0.88789, null, 0.19663, null, 0.77461, null, 0.56289, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2018-11-28", "Adult", "Adult", "Pancreas", "Endocrine 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": ["50713"], "units": {}, "query_ms": 8.003859999007545}