{"database": "metadata", "table": "run_metadata", "rows": [[71746, "SRR21966435", "SRX17949914", "SRS15467389", "SRP403311", "PRJNA891853", "Dendrimer targeted immunosuppression of microglia reactivity further enhances promotes photoreceptor regeneration kinetics in the zebrafish retina", "GSE216060", "Transcriptome Analysis", "We used a zebrafish model of inducible rod photoreceptor death and investsgate the effect of Dexamethasone and nanoparticle conjugated Dex on regeneration kinetics Overall design: We used bulk RNA seq to analyze expression of zebrafish eyes at 7 dpf that were untreated  treated with Mtz to kill rods  treated with Mtz + D Dex induce immunosupression or treated with D Dex alone", null, "pubmed:37202450", null, "MtzDDex Replicate 3", "GSM6658009", null, "source name:eye|tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:24h Mtz to ablate rods  then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection|age:7dpf", "MtzDDex Replicate 3", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:24h Mtz to ablate rods  then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection|age:7dpf", "GSM6658009", "GSM6658009: MtzDDex Replicate 3; Danio rerio; RNA Seq", "GSM6658009 r1", "GSM6658009", "1", "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4  Takara 634440 kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP403311", null, "loader:fastq load.py", "KEmm-Mtz-D-Dex-3_S6_L002_R1_001.fastq.gz", "fastq", 2883222900.0, 28832229.0, "GSM6658009 r2", "0:100", "A:773580885;C:673456442;G:648869453;T:787254197;N:61923", 100, null, null, null, 773580885, 673456442, 648869453, 787254197, 61923, "SRX17949914", "SRS15467389", "SRA1524004", "Mumm lab, Human Genetics, Johns Hopkins University", "Mumm lab, Human Genetics, Johns Hopkins University", 1, 0.92715, null, 0.14452, null, 0.6994, null, 0.4374, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "United States", "2022-10-18", "Larval", "Larval", "Eye", "Sensory 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": ["71746"], "units": {}, "query_ms": 21.524174997466616}