{"database": "metadata", "table": "run_metadata", "rows": [[41668, "SRR5115715", "SRX2431086", "SRS1866963", "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 \u201cPost Mitotic\u201d 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 \u00b5g 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  \u201cswitch like\u201d expression profiles  and that miRNA processing was also found important for reprogramming Conclusions:  We conclude that reprogramming of a \u201cpost mitotic\u201d 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.", null, "pubmed:29121865", null, "0 hpi rep1", "GSM2430654", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:0", "0 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: \u201c  b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments  and \u201c  max intron length\u201d of 400 kbs. Novel transcript discovery was not performed  employing \u201c  no coverage search\u201d and \u201c  no novel juncs\u201d 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: \u201c  multi read correct\u201d to adjust expression calculations for reads that map in more than one locus  as well as \u201c  compatible hits norm\u201d and \u201c  upper quartile \u2013norm\u201d 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", null, "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", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:0", "GSM2430654", "GSM2430654: 0 hpi rep1; Danio rerio; RNA Seq", "GSM2430654", null, "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:GSM2430654", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "0hpi_44113.fastq.gz", "fastq", 2656056728.0, 51078014.0, "GSM2430654 r1", "0:52", "A:652742098;C:649243306;G:612049135;T:741907471;N:114718", 52, null, null, null, 652742098, 649243306, 612049135, 741907471, 114718, "SRX2431086", "SRS1866963", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.85198, null, 0.24059, null, 0.73357, null, 0.48804, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"]], "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": ["41668"], "units": {}, "query_ms": 8.853467996232212}