run_metadata: 38046

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
38046	SRR1427469	SRX612649	SRS643610	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration		pubmed:25220904		28d	GSM1417152		source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	28d	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417152	GSM1417152: 28d; Danio rerio; miRNA Seq	GSM1417152		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417152	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP043465			28d.fq	bam	694299184.0	32089203.0	GSM1417152 r1	0:21.64 1:0	A:174747494;C:132129648;G:193085254;T:194336788;N:0	21	0			174747494	132129648	193085254	194336788	0	SRX612649	SRS643610	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.93434		0.05272		0.98831		0.56642		23		B		usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown		United States	2014-06-20	Adult	Adult	Eye	Sensory System