run_metadata: 61820
This data as json
| 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 |
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| 61820 | SRR12992433 | SRX9443933 | SRS7657857 | 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. | pubmed:33186559;pubmed:36012210 | T3dpa 1 | GSM4885966 | source name:caudal fin|treatment:caudal fin removal|time:3dpa|tissue:caudal fin regenerating | T3dpa 1 | Basecalls performed using Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ 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；2Random primed first strand cDNA synthesis；3dUTP 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:3dpa|tissue:caudal fin regenerating | GSM4885966 | GSM4885966: T3dpa 1; Danio rerio; RNA Seq | GSM4885966 | 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；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification. | GEO Accession:GSM4885966 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP291307 | S259_genedenovo-A_R1811229_AHC7LKDSXX_S259_L004_R1_001.fastq.gz S259_genedenovo-A_R1811229_AHC7LKDSXX_S259_L004_R2_001.fastq.gz | fastq fastq | 13480211400.0 | 44934038.0 | GSM4885966 r1 | 0:150 1:150 | A:3210397485;C:3465436442;G:3477077735;T:3327162280;N:137458 | 150 | 150 | 3210397485 | 3465436442 | 3477077735 | 3327162280 | 137458 | SRX9443933 | SRS7657857 | SRA1154680 | GEO | henan normal university | 2 | 0.90619 | 0.90739 | 0.26762 | 0.26385 | 0.73783 | 0.73701 | 0.58215 | 0.59258 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | China | 2020-11-05 | Undetermined | Undetermined | Fin | Surface Structure |