{"database": "metadata", "table": "run_metadata", "rows": [[61815, "SRR12992438", "SRX9443938", "SRS7657861", "SRP291307", "PRJNA674824", "Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology", "GSE160909", "Transcriptome Analysis", "Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.", null, "pubmed:33186559;pubmed:36012210", null, "T7dpa 3", "GSM4885971", null, "source name:caudal fin|treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating", "T7dpa 3", "Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5\u2019 3\u2019 adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt", "caudal fin", "Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.", "RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment\uff1b2Random primed first strand cDNA synthesis\uff1b3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.", "Wild type zebrafish were kept in a closed recirculating aquacultural system.", "treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating", "GSM4885971", "GSM4885971: T7dpa 3; Danio rerio; RNA Seq", "GSM4885971", null, "1", "RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment\uff1b2Random primed first strand cDNA synthesis\uff1b3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.", "GEO Accession:GSM4885971", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP291307", null, null, "S264_genedenovo-A_R1811235_AHC7LKDSXX_S264_L004_R1_001.fastq.gz S264_genedenovo-A_R1811235_AHC7LKDSXX_S264_L004_R2_001.fastq.gz", "fastq fastq", 12837992700.0, 42793309.0, "GSM4885971 r1", "0:150 1:150", "A:2967571445;C:3402582572;G:3367407968;T:3100298259;N:132456", 150, 150, null, null, 2967571445, 3402582572, 3367407968, 3100298259, 132456, "SRX9443938", "SRS7657861", "SRA1154680", "GEO", "henan normal university", 2, 0.92162, 0.92273, 0.24841, 0.2408, 0.74259, 0.74134, 0.57104, 0.55898, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-11-05", "Undetermined", "Undetermined", "Fin", "Surface Structure"]], "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": ["61815"], "units": {}, "query_ms": 9.796455007744953}