{"database": "metadata", "table": "run_metadata", "rows": [[44909, "SRR6293903", "SRX3395014", "SRS2689199", "SRP125042", "PRJNA418467", "Age related Islet Inflammation Marks the Proliferative Decline of Pancreatic Beta cells in Zebrafish", "GSE106938", "Transcriptome Analysis", "Individual organisms age at different rates  however  it remains unclear how aging alters the properties of individual cells.  Here we show that zebrafish pancreatic beta cells exhibit heterogeneity in both gene expression and proliferation with age.  Individual beta cells show marked variability in transcripts involved in endoplasmic reticulum stress  inhibition of growth factor signaling and inflammation  including NF kB signaling.  Using a reporter line  we show that NF kB signaling is indeed activated heterogeneously with age.  Notably  beta cells with higher NF kB activity proliferate less compared to neighbors with lower activity.  Furthermore  NF kB signalinghigh beta cells from younger islets upregulate socs2  a gene naturally expressed in beta cells from older islets.  In turn  socs2 can inhibit proliferation cell autonomously.  NF kB activation correlates with the recruitment of tnfa expressing immune cells  pointing towards a role for the islet microenvironment in this activity.  We propose that aging is heterogeneous across individual beta cells and identify NF kB signaling as a marker of heterogeneity. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from 3 mpf and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta cells using Quick RNA MicroPrep kit R1050 Zymo Research. Sequencing was performed on llumina HiSeq2500 in 2x75bp paired end mode. Reads were splice aligned to the zebrafish genome  GRCz10  using HISAT2. htseq count was used to assign reads to exons thus eventually getting counts per gene.", null, "pubmed:29624168", null, "3mpf rep1", "GSM2857830", null, "tissue:beta cells|age:3 month|strain:Tgins:BB1.0L", "3mpf rep1", "Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters sam files converted to bam using samtools Genome build: Zebrafish GRCz10 Supplementary files format and content: read counts were generated using htseq count", "beta cells", null, "FACS llumina HiSeq2500 in 2x75bp paired end mode", null, "age:3 month|strain:Tgins:BB1.0L", "GSM2857830", "GSM2857830: 3mpf rep1; Danio rerio; RNA Seq", "GSM2857830", null, "1", "FACS llumina HiSeq2500 in 2x75bp paired end mode", "GEO Accession:GSM2857830", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP125042", null, null, "L10758_Track-31235_R1.fastq.gz L10758_Track-31235_R2.fastq.gz", "fastq fastq", 4259609848.0, 28023749.0, "GSM2857830 r1", "0:76 1:76", "A:1095866394;C:1004201489;G:1014981602;T:1140141196;N:4419167", 76, 76, null, null, 1095866394, 1004201489, 1014981602, 1140141196, 4419167, "SRX3395014", "SRS2689199", "SRA631121", "GEO", "Ninov Lab, CRTD", 2, 0.87618, 0.87022, 0.1249, 0.12602, 0.76368, 0.76469, 0.65739, 0.64564, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2017-11-15", "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": ["44909"], "units": {}, "query_ms": 8.078238999587484}