{"database": "metadata", "table": "run_metadata", "rows": [[19504, "ERR14085273", "ERX13487665", "ERS22622320", "ERP167301", "PRJEB83711", "From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration", "inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243", "Other", "Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures  making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study  we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery.  Using RNA sequencing at four key time points: control  1 day post lesion  4 dpl  and 7 dpl  we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these  the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK  which modulates progenitor cell proliferation  differentiation  and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context.  This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair  further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans.", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", null, "RNA seq Control Replicate 2", "Control Replicate 2", "SAMEA117549420", "Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology", "ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009444 Control Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009444 Control Replicate 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration", "From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9525", "1", "1", "NaN", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167301", "Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "19153_C6_R1.fastq.gz 19154_C6_R2.fastq.gz", "fastq fastq", 11398526732.0, 37743466.0, "RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9525", "0:151 1:151", "A:3315198872;C:2268180334;G:2561003095;T:3244771542;N:9372889", 151, 151, null, null, 3315198872, 2268180334, 2561003095, 3244771542, 9372889, "ERX13487665", "ERS22622320", "ERA31046072", "Indian Biological Data Centre|European Nucleotide Archive", "Indian Biological Data Centre", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "India", "2024-12-19", "Undetermined", "Undetermined", "Brain", "Nervous 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": ["19504"], "units": {}, "query_ms": 10.252493011648767}