run_metadata: 51201

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
51201	SRR8587734	SRX5388273	SRS4376712	SRP186180	PRJNA523009	Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq	GSE126701	Transcriptome Analysis	Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq.	parent bioproject:PRJNA523007	pubmed:32106888		RNA fosl1aWT 4dpa rep1	GSM3611575		tissue:zebrafish fin\|cell type:blastema\|dy post amputation:4 dpa\|genotype/variation:fosl1a WT	RNA fosl1aWT 4dpa rep1	Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT	zebrafish fin		The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.		cell type:blastema\|dy post amputation:4 dpa\|genotype/variation:fosl1a WT	GSM3611575	GSM3611575: RNA fosl1aWT 4dpa rep1; Danio rerio; RNA Seq	GSM3611575		1	The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions.	GEO Accession:GSM3611575	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP186180			RNA_fosl1aWT_4dpa_rep1_R1.fastq.gz RNA_fosl1aWT_4dpa_rep1_R2.fastq.gz	fastq fastq	3896927850.0	25979519.0	GSM3611575 r1	0:75 1:75	A:940364294;C:1005241083;G:990216788;T:960643155;N:462530	75	75			940364294	1005241083	990216788	960643155	462530	SRX5388273	SRS4376712	SRA850124	GEO	Ting Wang, Department of Genetics, Washington University School of Medicine	2	0.94564	0.93465	0.04169	0.04145	0.74316	0.74757	0.45882	0.44998	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2019-02-18	Undetermined	Undetermined	Fin	Surface Structure