run_metadata: 55258

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
55258	SRR10204641	SRX6924590	SRS5455467	SRP223753	PRJNA575017	Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors	PRJNA575017	Other	In humans optic nerve damage caused by trauma or diseases such as glaucoma can result in permanent visual loss. The permanence of the damage is due to a failure of the human central nervous system CNS to support regenerative nerve growth. In contrast fish naturally respond to optic nerve injury by re establishing the growth capacity of CNS neurons and eventually recovering visual function. It is well known that the cellular programming regulating nerve growth and guidance in the developing visual system is highly conserved between fish and humans. Once the mature visual circuitry has been established the cells undergo a shift in programming from one that promotes the wiring of the visual system to one that promotes the transmittal of light information gathered in the retina to the brain where it is perceived as an image. Thus what appears to set fish apart from humans is their ability to reprogram adult retinal neurons for wiring in response to optic nerve injury. The goal of this study was to understand how adult retinal ganglion cells are reprogrammed for axon growth post optic nerve injury. We achieved this goal by coupling temporal analysis of gene expression with the identification of putative regulatory interactions over the full course of optic nerve regeneration in zebrafish. More specifically we conducted a temporal analysis of gene expression RNA Seq and chromatin accessibility ATAC Seq over the course of optic nerve regeneration in adult zebrafish. We used time points corresponding to different stages of axon regeneration post optic nerve crush: 2 xxx post injury dpi initial axon growth past the site of injury; 4 dpi growth across the midline; 7 dpi target selection; 12 dpi synaptogenesis.			Gene expression Danio rerio adult retina 2 days post optic nerve crush replicate 3	Gene expression Danio rerio adult retina 2 days post optic nerve crush replicate 3	Drerio 2dpi retina RNA 3		strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 2 dpi bio rep 3\|BioSampleModel:Model organism or animal									Gene expression Danio rerio adult retina 2 days post optic nerve crush replicate 3	Drerio UWM RGC 2RNA3	Drerio UWM RGC 2RNA3	RNA was extracted and purified from retinas dissected from adult fish 2 days post optic nerve crush. RNA was extracted from pooled retinas using the RNeasy Micro kit Qiagen and concentrated using the RNA Clean & Concentrator kit Zymo.cDNA libraries were generated for each RNA sample using Tru Seq Stranded Total & mRNA Sample Prep Kits Illumina 20020595. Each cDNA library was indexed for multiplexing and subsequently sequenced on four lanes of the Illumina Hiseq2000. Libraries were sequenced at 50 bp 3040 million paired end reads/sample			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP223753			2RNA3_R2.fastq.gz 2RNA3_R1.fastq.gz	fastq fastq	6785206362.0	66521631.0	2RNA3 R1.fastq.gz	0:51 1:51	A:1912390199;C:1464364012;G:1461265105;T:1935814275;N:11372771	51	51			1912390199	1464364012	1461265105	1935814275	11372771	SRX6924590	SRS5455467	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.93368	0.93815	0.19386	0.19425	0.73594	0.73789	0.69561	0.68564	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown		United States	2019-09-30	Adult	Adult	Eye	Sensory System