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 41655,SRR5115728,SRX2431099,SRS1866976,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,,18 hpi rep5,GSM2430667,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18,18 hpi rep5,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:18,GSM2430667,GSM2430667: 18 hpi rep5; Danio rerio; RNA Seq,GSM2430667,,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:GSM2430667,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,18hpi_54366.fastq.gz,fastq,3043532908.0,58529479.0,GSM2430667 r1,0:52,A:729034781;C:769509924;G:743085356;T:801831768;N:71079,52,,,,729034781,769509924,743085356,801831768,71079,SRX2431099,SRS1866976,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.73906,,0.22225,,0.74061,,0.49988,,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 41656,SRR5115727,SRX2431098,SRS1866975,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,,18 hpi rep4,GSM2430666,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18,18 hpi rep4,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:18,GSM2430666,GSM2430666: 18 hpi rep4; Danio rerio; RNA Seq,GSM2430666,,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:GSM2430666,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,18hpi_48592.fastq.gz,fastq,2622132240.0,50425620.0,GSM2430666 r1,0:52,A:566371236;C:777180578;G:659521124;T:618999154;N:60148,52,,,,566371236,777180578,659521124,618999154,60148,SRX2431098,SRS1866975,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.92057,,0.28475,,0.86833,,0.72823,,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 41657,SRR5115726,SRX2431097,SRS1866974,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,,18 hpi rep3,GSM2430665,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18,18 hpi rep3,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:18,GSM2430665,GSM2430665: 18 hpi rep3; Danio rerio; RNA Seq,GSM2430665,,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:GSM2430665,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,18hpi_48591.fastq.gz,fastq,2478119176.0,47656138.0,GSM2430665 r1,0:52,A:493736890;C:768557459;G:661870968;T:553896608;N:57251,52,,,,493736890,768557459,661870968,553896608,57251,SRX2431097,SRS1866974,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.96537,,0.26164,,0.87892,,0.7204,,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 41658,SRR5115725,SRX2431096,SRS1866973,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,,18 hpi rep2,GSM2430664,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18,18 hpi rep2,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:18,GSM2430664,GSM2430664: 18 hpi rep2; Danio rerio; RNA Seq,GSM2430664,,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:GSM2430664,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,18hpi_48590.fastq.gz,fastq,2414695452.0,46436451.0,GSM2430664 r1,0:52,A:475090050;C:755838280;G:657771658;T:525939134;N:56330,52,,,,475090050,755838280,657771658,525939134,56330,SRX2431096,SRS1866973,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.9654,,0.26982,,0.89676,,0.72161,,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 41659,SRR5115724,SRX2431095,SRS1866972,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,,18 hpi rep1,GSM2430663,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18,18 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:18,GSM2430663,GSM2430663: 18 hpi rep1; Danio rerio; RNA Seq,GSM2430663,,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:GSM2430663,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,18hpi_48589.fastq.gz,fastq,2275983060.0,43768905.0,GSM2430663 r1,0:52,A:466133336;C:694614756;G:598071579;T:517110546;N:52843,52,,,,466133336,694614756,598071579,517110546,52843,SRX2431095,SRS1866972,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.94909,,0.2695,,0.86809,,0.70019,,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 41660,SRR5115723,SRX2431094,SRS1866971,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 rep5,GSM2430662,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9,9 hpi rep5,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,GSM2430662,GSM2430662: 9 hpi rep5; Danio rerio; RNA Seq,GSM2430662,,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:GSM2430662,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,9hpi_54368.fastq.gz,fastq,2831111348.0,54444449.0,GSM2430662 r1,0:52,A:674270099;C:713818041;G:694997603;T:747958840;N:66765,52,,,,674270099,713818041,694997603,747958840,66765,SRX2431094,SRS1866971,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.81449,,0.24117,,0.74091,,0.53961,,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 41661,SRR5115722,SRX2431093,SRS1866970,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 rep4,GSM2430661,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9,9 hpi rep4,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,GSM2430661,GSM2430661: 9 hpi rep4; Danio rerio; RNA Seq,GSM2430661,,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:GSM2430661,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,9hpi_48586.fastq.gz,fastq,3247890880.0,62459440.0,GSM2430661 r1,0:52,A:737775958;C:866361850;G:806031275;T:837644754;N:77043,52,,,,737775958,866361850,806031275,837644754,77043,SRX2431093,SRS1866970,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.88824,,0.26531,,0.77619,,0.64707,,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 41662,SRR5115721,SRX2431092,SRS1866969,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 rep3,GSM2430660,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9,9 hpi rep3,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,GSM2430660,GSM2430660: 9 hpi rep3; Danio rerio; RNA Seq,GSM2430660,,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:GSM2430660,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,9hpi_48585.fastq.gz,fastq,2383588948.0,45838249.0,GSM2430660 r1,0:52,A:471509922;C:736118462;G:639172021;T:536732824;N:55719,52,,,,471509922,736118462,639172021,536732824,55719,SRX2431092,SRS1866969,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.96831,,0.25406,,0.88327,,0.69186,,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 41663,SRR5115720,SRX2431091,SRS1866968,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 rep2,GSM2430659,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9,9 hpi rep2,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,GSM2430659,GSM2430659: 9 hpi rep2; Danio rerio; RNA Seq,GSM2430659,,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:GSM2430659,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,9hpi_48584.fastq.gz,fastq,2858494184.0,54971042.0,GSM2430659 r1,0:52,A:601123087;C:841668883;G:744364922;T:671270980;N:66312,52,,,,601123087,841668883,744364922,671270980,66312,SRX2431091,SRS1866968,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.93531,,0.28407,,0.86277,,0.73297,,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 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 41665,SRR5115718,SRX2431089,SRS1866966,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,,0 hpi rep4,GSM2430657,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:0,0 hpi rep4,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:0,GSM2430657,GSM2430657: 0 hpi rep4; Danio rerio; RNA Seq,GSM2430657,,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:GSM2430657,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,0hpi_54367.fastq.gz,fastq,3737365060.0,71872405.0,GSM2430657 r1,0:52,A:898855616;C:929504130;G:883445728;T:1025471492;N:88094,52,,,,898855616,929504130,883445728,1025471492,88094,SRX2431089,SRS1866966,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.80824,,0.21971,,0.75511,,0.45635,,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 41666,SRR5115717,SRX2431088,SRS1866965,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,,0 hpi rep3,GSM2430656,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:0,0 hpi rep3,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:0,GSM2430656,GSM2430656: 0 hpi rep3; Danio rerio; RNA Seq,GSM2430656,,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:GSM2430656,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,0hpi_54365.fastq.gz,fastq,2479423440.0,47681220.0,GSM2430656 r1,0:52,A:585035619;C:641794408;G:600148220;T:652388942;N:56251,52,,,,585035619,641794408,600148220,652388942,56251,SRX2431088,SRS1866965,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.7459,,0.20704,,0.76674,,0.44617,,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 41667,SRR5115716,SRX2431087,SRS1866964,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,,0 hpi rep2,GSM2430655,,source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:0,0 hpi rep2,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:0,GSM2430655,GSM2430655: 0 hpi rep2; Danio rerio; RNA Seq,GSM2430655,,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:GSM2430655,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP095238,,,0hpi_48587.fastq.gz,fastq,2251744196.0,43302773.0,GSM2430655 r1,0:52,A:446930339;C:692500195;G:602614693;T:509646110;N:52859,52,,,,446930339,692500195,602614693,509646110,52859,SRX2431087,SRS1866964,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.96295,,0.25309,,0.90035,,0.717,,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 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 “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,,0 hpi rep1,GSM2430654,,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: “ 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:0,GSM2430654,GSM2430654: 0 hpi rep1; Danio rerio; RNA Seq,GSM2430654,,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,,SRP095238,,,0hpi_44113.fastq.gz,fastq,2656056728.0,51078014.0,GSM2430654 r1,0:52,A:652742098;C:649243306;G:612049135;T:741907471;N:114718,52,,,,652742098,649243306,612049135,741907471,114718,SRX2431086,SRS1866963,SRA504806,GEO,"Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan",1,0.85198,,0.24059,,0.73357,,0.48804,,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 74907,SRR24130494,SRX19929339,SRS17279406,SRP431990,PRJNA954363,Biallelic variants in CSPG4 cause a novel neurodevelopmental disorder with intellectual disability global developmental delay and facial anomalies,GSE229401,Transcriptome Analysis,We aimed to define a novel autosomal recessive neurodevelopmental disorder characterize its clinical features and identify the underlying genetic cause for this condition. Clinical and genetic data from affected individuals with neurological disorders were matched across families from five global sites. Here we report five recessive CSPG4 NM 001897 missense variants [three homozygous: c.A1370G p.Asp457Gly c.2627G>A p.Arg876His and c.3247C>A p.Gln1083Lys and two compound heterozygous: c.A1370G and c.5156A>G p.Asp457Gly and p.Gln1719Arg and c.658A>G and c.1220 1221delinsTG p.Thr220Ala and p.Pro407Leu] by next generation sequencing of five unrelated families with seven affected subjects. All subjects share a novel neurodevelopmental syndrome characterized by severe intellectual disability global developmental delay delayed ability to walk speech and language delay distinctive facial features along with varying degrees of neurological impairment including hypotonia cerebellar hypoplasia and/or seizures. All CSPG4 variants were predicted to be damaging using in silico tools and three dimensional molecular modeling suggested significant alterations in protein stability compromising inter and intra molecular interactions. The impact on neurological and craniofacial development was analyzed in CRISPR/Cas9 mediated zebrafish models. CSPG4 variants affected notochord development neuronal function and cerebellar structure along with a disorganized head scaffold with anomalous skeletal and cartilage components. Two individuals metabolomics and crispant transcriptomics revealed significant perturbation of metabolites extracellular matrix ECM regulating pathways and genes previously described to cause mental retardation dwarfism and facial anomalies in humans. Our study links novel rare damaging variants of the ECM gene CSPG4 to a novel recessive Mendelian neurodevelopmental disorder in humans and supports the role of CSPG4 in early development. Overall design: Zebrafish CSPG4 model RNA sequencing. We used RNA sequencing of dissected heads from n=20 animals of each group in 3 independent replicates.,,,,CSPG4 Crispant Sample 2,GSM7162843,,source name:pooled heads|tissue:pooled heads|treatment:CSPG4 sgRNA Cas9|geo loc name:missing|collection date:missing,CSPG4 Crispant Sample 2,Reads were mapped to the Danio rerio GRCz11 Genome Reference Consortium Zebrafish Build 11 INSDC Assembly GCA 000002035.4 May 2017using STAR 2.6.1d aligner HTSeq count v0.9.1 was used to generate the raw counts. We used Limma voom to normalize the raw counts. Differentially expressed genes DEGs between zebrafish CSPG4 model and WT controls were identified as described previously Unlu Qi et al. 2020. Data in fastq format were mapped to the zebrafish Danio rerio genome assembly GRCz11 danRer11 [https://www.ncbi.nlm.nih.gov/grc/zebrafish] using STAR aligner v2.6.1d [https://github.com/alexdobin/STAR]. Reads were summarized using Counts v2.0.0 [http://subread.sourceforge.net/]. Differential expression analysis was performed using the limma package [https://bioconductor.org/packages/release/bioc/html/limma.html] and gene set enrichment analysis GSEA was performed using Cluster Profiler package [https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html]. Assembly: GRCz11 Supplementary files format and content: Gene list Supplemental Table 2.xls SPG4 ZF CRISPANTS LEX8 Rawcounts.tsv,pooled heads,,mRNA libraries were prepared using Lexogen QuantSeq 3’ mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,tissue:pooled heads|treatment:CSPG4 sgRNA Cas9,GSM7162843,GSM7162843: CSPG4 Crispant Sample 2; Danio rerio; RNA Seq,GSM7162843 r1,GSM7162843,1,mRNA libraries were prepared using Lexogen QuantSeq three prime mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP431990,,,CSP_G2_CR2_R1.fastq.gz,fastq,861937204.0,11341279.0,GSM7162843 r1,0:76 1:0,A:255753716;C:175165107;G:186784144;T:244229406;N:4831,76,0,,,255753716,175165107,186784144,244229406,4831,SRX19929339,SRS17279406,SRA1622718,Sidra Medicine,Sidra Medicine,1,0.84349,,0.20083,,0.76049,,0.61192,,76,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Qatar,2023-04-11,Undetermined,Undetermined,Head,Nervous System 74908,SRR24130495,SRX19929338,SRS17279405,SRP431990,PRJNA954363,Biallelic variants in CSPG4 cause a novel neurodevelopmental disorder with intellectual disability global developmental delay and facial anomalies,GSE229401,Transcriptome Analysis,We aimed to define a novel autosomal recessive neurodevelopmental disorder characterize its clinical features and identify the underlying genetic cause for this condition. Clinical and genetic data from affected individuals with neurological disorders were matched across families from five global sites. Here we report five recessive CSPG4 NM 001897 missense variants [three homozygous: c.A1370G p.Asp457Gly c.2627G>A p.Arg876His and c.3247C>A p.Gln1083Lys and two compound heterozygous: c.A1370G and c.5156A>G p.Asp457Gly and p.Gln1719Arg and c.658A>G and c.1220 1221delinsTG p.Thr220Ala and p.Pro407Leu] by next generation sequencing of five unrelated families with seven affected subjects. All subjects share a novel neurodevelopmental syndrome characterized by severe intellectual disability global developmental delay delayed ability to walk speech and language delay distinctive facial features along with varying degrees of neurological impairment including hypotonia cerebellar hypoplasia and/or seizures. All CSPG4 variants were predicted to be damaging using in silico tools and three dimensional molecular modeling suggested significant alterations in protein stability compromising inter and intra molecular interactions. The impact on neurological and craniofacial development was analyzed in CRISPR/Cas9 mediated zebrafish models. CSPG4 variants affected notochord development neuronal function and cerebellar structure along with a disorganized head scaffold with anomalous skeletal and cartilage components. Two individuals metabolomics and crispant transcriptomics revealed significant perturbation of metabolites extracellular matrix ECM regulating pathways and genes previously described to cause mental retardation dwarfism and facial anomalies in humans. Our study links novel rare damaging variants of the ECM gene CSPG4 to a novel recessive Mendelian neurodevelopmental disorder in humans and supports the role of CSPG4 in early development. Overall design: Zebrafish CSPG4 model RNA sequencing. We used RNA sequencing of dissected heads from n=20 animals of each group in 3 independent replicates.,,,,CSPG4 Crispant Sample 1,GSM7162842,,source name:pooled heads|tissue:pooled heads|treatment:CSPG4 sgRNA Cas9|geo loc name:missing|collection date:missing,CSPG4 Crispant Sample 1,Reads were mapped to the Danio rerio GRCz11 Genome Reference Consortium Zebrafish Build 11 INSDC Assembly GCA 000002035.4 May 2017using STAR 2.6.1d aligner HTSeq count v0.9.1 was used to generate the raw counts. We used Limma voom to normalize the raw counts. Differentially expressed genes DEGs between zebrafish CSPG4 model and WT controls were identified as described previously Unlu Qi et al. 2020. Data in fastq format were mapped to the zebrafish Danio rerio genome assembly GRCz11 danRer11 [https://www.ncbi.nlm.nih.gov/grc/zebrafish] using STAR aligner v2.6.1d [https://github.com/alexdobin/STAR]. Reads were summarized using Counts v2.0.0 [http://subread.sourceforge.net/]. Differential expression analysis was performed using the limma package [https://bioconductor.org/packages/release/bioc/html/limma.html] and gene set enrichment analysis GSEA was performed using Cluster Profiler package [https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html]. Assembly: GRCz11 Supplementary files format and content: Gene list Supplemental Table 2.xls SPG4 ZF CRISPANTS LEX8 Rawcounts.tsv,pooled heads,,mRNA libraries were prepared using Lexogen QuantSeq 3’ mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,tissue:pooled heads|treatment:CSPG4 sgRNA Cas9,GSM7162842,GSM7162842: CSPG4 Crispant Sample 1; Danio rerio; RNA Seq,GSM7162842 r1,GSM7162842,1,mRNA libraries were prepared using Lexogen QuantSeq three prime mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP431990,,,CSP_G2_CR1_R1.fastq.gz,fastq,901946416.0,11867716.0,GSM7162842 r1,0:76 1:0,A:258637768;C:182022028;G:198476522;T:262805091;N:5007,76,0,,,258637768,182022028,198476522,262805091,5007,SRX19929338,SRS17279405,SRA1622718,Sidra Medicine,Sidra Medicine,1,0.79839,,0.19613,,0.75958,,0.58366,,76,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Qatar,2023-04-11,Undetermined,Undetermined,Head,Nervous System 74909,SRR24130496,SRX19929337,SRS17279404,SRP431990,PRJNA954363,Biallelic variants in CSPG4 cause a novel neurodevelopmental disorder with intellectual disability global developmental delay and facial anomalies,GSE229401,Transcriptome Analysis,We aimed to define a novel autosomal recessive neurodevelopmental disorder characterize its clinical features and identify the underlying genetic cause for this condition. Clinical and genetic data from affected individuals with neurological disorders were matched across families from five global sites. Here we report five recessive CSPG4 NM 001897 missense variants [three homozygous: c.A1370G p.Asp457Gly c.2627G>A p.Arg876His and c.3247C>A p.Gln1083Lys and two compound heterozygous: c.A1370G and c.5156A>G p.Asp457Gly and p.Gln1719Arg and c.658A>G and c.1220 1221delinsTG p.Thr220Ala and p.Pro407Leu] by next generation sequencing of five unrelated families with seven affected subjects. All subjects share a novel neurodevelopmental syndrome characterized by severe intellectual disability global developmental delay delayed ability to walk speech and language delay distinctive facial features along with varying degrees of neurological impairment including hypotonia cerebellar hypoplasia and/or seizures. All CSPG4 variants were predicted to be damaging using in silico tools and three dimensional molecular modeling suggested significant alterations in protein stability compromising inter and intra molecular interactions. The impact on neurological and craniofacial development was analyzed in CRISPR/Cas9 mediated zebrafish models. CSPG4 variants affected notochord development neuronal function and cerebellar structure along with a disorganized head scaffold with anomalous skeletal and cartilage components. Two individuals metabolomics and crispant transcriptomics revealed significant perturbation of metabolites extracellular matrix ECM regulating pathways and genes previously described to cause mental retardation dwarfism and facial anomalies in humans. Our study links novel rare damaging variants of the ECM gene CSPG4 to a novel recessive Mendelian neurodevelopmental disorder in humans and supports the role of CSPG4 in early development. Overall design: Zebrafish CSPG4 model RNA sequencing. We used RNA sequencing of dissected heads from n=20 animals of each group in 3 independent replicates.,,,,CSPG4 Control 2,GSM7162841,,source name:pooled heads|tissue:pooled heads|treatment:wildtype|geo loc name:missing|collection date:missing,CSPG4 Control 2,Reads were mapped to the Danio rerio GRCz11 Genome Reference Consortium Zebrafish Build 11 INSDC Assembly GCA 000002035.4 May 2017using STAR 2.6.1d aligner HTSeq count v0.9.1 was used to generate the raw counts. We used Limma voom to normalize the raw counts. Differentially expressed genes DEGs between zebrafish CSPG4 model and WT controls were identified as described previously Unlu Qi et al. 2020. Data in fastq format were mapped to the zebrafish Danio rerio genome assembly GRCz11 danRer11 [https://www.ncbi.nlm.nih.gov/grc/zebrafish] using STAR aligner v2.6.1d [https://github.com/alexdobin/STAR]. Reads were summarized using Counts v2.0.0 [http://subread.sourceforge.net/]. Differential expression analysis was performed using the limma package [https://bioconductor.org/packages/release/bioc/html/limma.html] and gene set enrichment analysis GSEA was performed using Cluster Profiler package [https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html]. Assembly: GRCz11 Supplementary files format and content: Gene list Supplemental Table 2.xls SPG4 ZF CRISPANTS LEX8 Rawcounts.tsv,pooled heads,,mRNA libraries were prepared using Lexogen QuantSeq 3’ mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,tissue:pooled heads|treatment:wildtype,GSM7162841,GSM7162841: CSPG4 Control 2; Danio rerio; RNA Seq,GSM7162841 r1,GSM7162841,1,mRNA libraries were prepared using Lexogen QuantSeq three prime mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP431990,,,CSP_CR_C2_R1.fastq.gz,fastq,881288324.0,11595899.0,GSM7162841 r1,0:76 1:0,A:262460545;C:180443987;G:195444043;T:242934708;N:5041,76,0,,,262460545,180443987,195444043,242934708,5041,SRX19929337,SRS17279404,SRA1622718,Sidra Medicine,Sidra Medicine,1,0.71545,,0.09599,,0.78182,,0.46812,,76,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Qatar,2023-04-11,Undetermined,Undetermined,Head,Nervous System 74910,SRR24130497,SRX19929336,SRS17279403,SRP431990,PRJNA954363,Biallelic variants in CSPG4 cause a novel neurodevelopmental disorder with intellectual disability global developmental delay and facial anomalies,GSE229401,Transcriptome Analysis,We aimed to define a novel autosomal recessive neurodevelopmental disorder characterize its clinical features and identify the underlying genetic cause for this condition. Clinical and genetic data from affected individuals with neurological disorders were matched across families from five global sites. Here we report five recessive CSPG4 NM 001897 missense variants [three homozygous: c.A1370G p.Asp457Gly c.2627G>A p.Arg876His and c.3247C>A p.Gln1083Lys and two compound heterozygous: c.A1370G and c.5156A>G p.Asp457Gly and p.Gln1719Arg and c.658A>G and c.1220 1221delinsTG p.Thr220Ala and p.Pro407Leu] by next generation sequencing of five unrelated families with seven affected subjects. All subjects share a novel neurodevelopmental syndrome characterized by severe intellectual disability global developmental delay delayed ability to walk speech and language delay distinctive facial features along with varying degrees of neurological impairment including hypotonia cerebellar hypoplasia and/or seizures. All CSPG4 variants were predicted to be damaging using in silico tools and three dimensional molecular modeling suggested significant alterations in protein stability compromising inter and intra molecular interactions. The impact on neurological and craniofacial development was analyzed in CRISPR/Cas9 mediated zebrafish models. CSPG4 variants affected notochord development neuronal function and cerebellar structure along with a disorganized head scaffold with anomalous skeletal and cartilage components. Two individuals metabolomics and crispant transcriptomics revealed significant perturbation of metabolites extracellular matrix ECM regulating pathways and genes previously described to cause mental retardation dwarfism and facial anomalies in humans. Our study links novel rare damaging variants of the ECM gene CSPG4 to a novel recessive Mendelian neurodevelopmental disorder in humans and supports the role of CSPG4 in early development. Overall design: Zebrafish CSPG4 model RNA sequencing. We used RNA sequencing of dissected heads from n=20 animals of each group in 3 independent replicates.,,,,CSPG4 Control 1,GSM7162840,,source name:pooled heads|tissue:pooled heads|treatment:wildtype|geo loc name:missing|collection date:missing,CSPG4 Control 1,Reads were mapped to the Danio rerio GRCz11 Genome Reference Consortium Zebrafish Build 11 INSDC Assembly GCA 000002035.4 May 2017using STAR 2.6.1d aligner HTSeq count v0.9.1 was used to generate the raw counts. We used Limma voom to normalize the raw counts. Differentially expressed genes DEGs between zebrafish CSPG4 model and WT controls were identified as described previously Unlu Qi et al. 2020. Data in fastq format were mapped to the zebrafish Danio rerio genome assembly GRCz11 danRer11 [https://www.ncbi.nlm.nih.gov/grc/zebrafish] using STAR aligner v2.6.1d [https://github.com/alexdobin/STAR]. Reads were summarized using Counts v2.0.0 [http://subread.sourceforge.net/]. Differential expression analysis was performed using the limma package [https://bioconductor.org/packages/release/bioc/html/limma.html] and gene set enrichment analysis GSEA was performed using Cluster Profiler package [https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html]. Assembly: GRCz11 Supplementary files format and content: Gene list Supplemental Table 2.xls SPG4 ZF CRISPANTS LEX8 Rawcounts.tsv,pooled heads,,mRNA libraries were prepared using Lexogen QuantSeq 3’ mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,tissue:pooled heads|treatment:wildtype,GSM7162840,GSM7162840: CSPG4 Control 1; Danio rerio; RNA Seq,GSM7162840 r1,GSM7162840,1,mRNA libraries were prepared using Lexogen QuantSeq three prime mRNA Seq Library Prep Kit according to manufacturer's protocols. three prime mRNA Seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP431990,,,CSP_CR_C1_R1.fastq.gz,fastq,798728080.0,10509580.0,GSM7162840 r1,0:76 1:0,A:233453016;C:163357112;G:175759009;T:226154417;N:4526,76,0,,,233453016,163357112,175759009,226154417,4526,SRX19929336,SRS17279403,SRA1622718,Sidra Medicine,Sidra Medicine,1,0.79246,,0.11025,,0.77053,,0.5668,,76,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Qatar,2023-04-11,Undetermined,Undetermined,Head,Nervous System