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
33123,SRR29672615,SRX25176099,SRS21866000,SRP517393,PRJNA1130538,ac4C transcriptomes of Zebrafish and Worm,GSE271258,Other,ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution  we performed ac4C RIP seq on Zebrafish and Worm.,,,,Zebrafish ac4C,GSM8372406,,tissue:Animal organ cells|cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215|geo loc name:missing|collection date:missing,Zebrafish ac4C,The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2   and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq  the mRNA expression level was analyzed by StringTie  and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format  containing the expression levels and ac4C status changes for each gene.,Animal organ cells,,Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched,,cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C  Abcam  catalog No. ab252215,GSM8372406,GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq,GSM8372406 r1,GSM8372406,1,Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP517393,,,Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz,fastq fastq,816231517.0,3830403.0,GSM8372406 r1,0:102.34 1:110.76,A:199381841;C:207571478;G:205740791;T:203535549;N:1858,102,110,,,199381841,207571478,205740791,203535549,1858,SRX25176099,SRS21866000,SRA1914369,Fujian Medical University,Fujian Medical University,2,0.60415,0.60545,0.08824,0.08794,0.78796,0.78733,0.43432,0.43842,126,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-01,Undetermined,Undetermined,Undetermined,Undetermined