{"database": "metadata", "table": "run_metadata", "rows": [[9345, "ERR2935790", "ERX2938584", "ERS2922620", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach  firstly  fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage  respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration  Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation  respectively. Firstly  fish were anesthetized by Tricaine. Once fish were immobilized  the caudal fin of each fish were resected  and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues  their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Cnt mRNA ML 2", "SAMEA5138253", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138253|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 2|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:Cnt mRNA ML 2 p", "Cnt mRNA ML 2 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach  firstly  fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage  respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration  Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation  respectively. Firstly  fish were anesthetized by Tricaine. Once fish were immobilized  the caudal fin of each fish were resected  and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues  their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN.  The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:0|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "Cnt-mRNA-ML-2_1.fastq.gz Cnt-mRNA-ML-2_2.fastq.gz", "fastq fastq", 13001272960.0, 81257956.0, "E MTAB 7464:Cnt mRNA ML 2 ", "0:80 1:80", "A:3429977204;C:2902807573;G:3288394622;T:3376870832;N:3222729", 80, 80, null, null, 3429977204, 2902807573, 3288394622, 3376870832, 3222729, "ERX2938584", "ERS2922620", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.89439, 0.89378, 0.3049, 0.30551, 0.75771, 0.76761, 0.52718, 0.52248, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-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": ["9345"], "units": {}, "query_ms": 10.855689999516471}