run_metadata: 41664

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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
41664	SRR5115719	SRX2431090	SRS1866967	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.		pubmed:29121865		9 hpi rep1	GSM2430658		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep1	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430658	GSM2430658: 9 hpi rep1; Danio rerio; RNA Seq	GSM2430658		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430658	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48583.fastq.gz	fastq	2348023808.0	45154304.0	GSM2430658 r1	0:52	A:520788777;C:655035758;G:589264364;T:582879912;N:54997	52				520788777	655035758	589264364	582879912	54997	SRX2431090	SRS1866967	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.90637		0.26958		0.80649		0.68165		52		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown		United States	2016-12-16	Undetermined	Adult	Head	Nervous System