metadata: run_metadata: 15 rows where experiment.library_selection = "other", experiment.library_source = "TRANSCRIPTOMIC" and tissue

15 rows where experiment.library_selection = "other", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Eye"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
55249	55249	SRR10204631	SRX6924600	SRS5455477	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 12 days post optic nerve crush replicate 3	Gene expression Danio rerio adult retina 12 days post optic nerve crush replicate 3	Drerio 12dpi retina RNA 3	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 12 dpi bio rep 3\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 12 days post optic nerve crush replicate 3	Drerio UWM RGC 12RNA3	Drerio UWM RGC 12RNA3	RNA was extracted and purified from retinas dissected from adult fish 12 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	12RNA3_R2.fastq.gz 12RNA3_R1.fastq.gz	fastq fastq	7100238666.0	69610183.0	12RNA3 R1.fastq.gz	0:51 1:51	A:1994877833;C:1522835113;G:1536004096;T:2034542295;N:11979329	51	51	1994877833	1522835113	1536004096	2034542295	11979329	SRX6924600	SRS5455477	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.91864	0.92256	0.22279	0.2214	0.71056	0.71033	0.58302	0.58156	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
55250	55250	SRR10204632	SRX6924599	SRS5455476	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 12 days post optic nerve crush replicate 2	Gene expression Danio rerio adult retina 12 days post optic nerve crush replicate 2	Drerio 12dpi retina RNA 2	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 12 dpi bio rep 2\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 12 days post optic nerve crush replicate 2	Drerio UWM RGC 12RNA2	Drerio UWM RGC 12RNA2	RNA was extracted and purified from retinas dissected from adult fish 12 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	12RNA2_R1.fastq.gz 12RNA2_R2.fastq.gz	fastq fastq	7137458364.0	69975082.0	12RNA2 R1.fastq.gz	0:51 1:51	A:2007595769;C:1534483902;G:1536122712;T:2047239325;N:12016656	51	51	2007595769	1534483902	1536122712	2047239325	12016656	SRX6924599	SRS5455476	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.92552	0.93193	0.19756	0.19742	0.73442	0.73486	0.62198	0.624	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
55251	55251	SRR10204633	SRX6924598	SRS5455475	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 12 days post optic nerve crush replicate 1	Gene expression Danio rerio adult retina 12 days post optic nerve crush replicate 1	Drerio 12dpi retina RNA 1	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 12 dpi bio rep 1\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 12 days post optic nerve crush replicate 1	Drerio UWM RGC 12RNA1	Drerio UWM RGC 12RNA1	RNA was extracted and purified from retinas dissected from adult fish 12 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	12RNA1_R1.fastq.gz 12RNA1_R2.fastq.gz	fastq fastq	6982997928.0	68460764.0	12RNA1 R1.fastq.gz	0:51 1:51	A:1937424944;C:1525219396;G:1543047188;T:1965619468;N:11686932	51	51	1937424944	1525219396	1543047188	1965619468	11686932	SRX6924598	SRS5455475	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.92729	0.92725	0.18199	0.17857	0.7387	0.74016	0.62519	0.65177	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
55252	55252	SRR10204634	SRX6924597	SRS5455474	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 7 days post optic nerve crush replicate 3	Gene expression Danio rerio adult retina 7 days post optic nerve crush replicate 3	Drerio 7dpi retina RNA 3	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 7 dpi bio rep 3\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 7 days post optic nerve crush replicate 3	Drerio UWM RGC 7RNA3	Drerio UWM RGC 7RNA3	RNA was extracted and purified from retinas dissected from adult fish 7 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	7RNA3_R1.fastq.gz 7RNA3_R2.fastq.gz	fastq fastq	7449627426.0	73035563.0	7RNA3 R1.fastq.gz	0:51 1:51	A:2076382757;C:1614609414;G:1624604001;T:2121529997;N:12501257	51	51	2076382757	1614609414	1624604001	2121529997	12501257	SRX6924597	SRS5455474	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.9268	0.93191	0.20459	0.20417	0.7094	0.71206	0.59551	0.59689	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
55253	55253	SRR10204635	SRX6924596	SRS5455473	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 7 days post optic nerve crush replicate 2	Gene expression Danio rerio adult retina 7 days post optic nerve crush replicate 2	Drerio 7dpi retina RNA 2	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 7 dpi bio rep 2\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 7 days post optic nerve crush replicate 2	Drerio UWM RGC 7RNA2	Drerio UWM RGC 7RNA2	RNA was extracted and purified from retinas dissected from adult fish 7 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	7RNA2_R1.fastq.gz 7RNA2_R2.fastq.gz	fastq fastq	7341157464.0	71972132.0	7RNA2 R1.fastq.gz	0:51 1:51	A:2049450846;C:1599496981;G:1597737251;T:2082196326;N:12276060	51	51	2049450846	1599496981	1597737251	2082196326	12276060	SRX6924596	SRS5455473	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.92912	0.93435	0.17783	0.17685	0.70972	0.711	0.63029	0.64014	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
55254	55254	SRR10204636	SRX6924595	SRS5455472	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 7 days post optic nerve crush replicate 1	Gene expression Danio rerio adult retina 7 days post optic nerve crush replicate 1	Drerio 7dpi retina RNA 1	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 7 dpi bio rep 1\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 7 days post optic nerve crush replicate 1	Drerio UWM RGC 7RNA1	Drerio UWM RGC 7RNA1	RNA was extracted and purified from retinas dissected from adult fish 7 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	7RNA1_R1.fastq.gz 7RNA1_R2.fastq.gz	fastq fastq	7243600482.0	71015691.0	7RNA1 R1.fastq.gz	0:51 1:51	A:2022470231;C:1565733898;G:1582218874;T:2060984226;N:12193253	51	51	2022470231	1565733898	1582218874	2060984226	12193253	SRX6924595	SRS5455472	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.92732	0.93289	0.20372	0.20499	0.71563	0.71747	0.62176	0.61991	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
55255	55255	SRR10204637	SRX6924594	SRS5455471	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 4 days post optic nerve crush replicate 3	Gene expression Danio rerio adult retina 4 days post optic nerve crush replicate 3	Drerio 4dpi retina RNA 3	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 4 dpi bio rep 3\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 4 days post optic nerve crush replicate 3	Drerio UWM RGC 4RNA3	Drerio UWM RGC 4RNA3	RNA was extracted and purified from retinas dissected from adult fish 4 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	4RNA3_R1.fastq.gz 4RNA3_R2.fastq.gz	fastq fastq	6967212408.0	68306004.0	4RNA3 R1.fastq.gz	0:51 1:51	A:1959619379;C:1495523948;G:1518029497;T:1982431365;N:11608219	51	51	1959619379	1495523948	1518029497	1982431365	11608219	SRX6924594	SRS5455471	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.92943	0.93378	0.19349	0.19204	0.7204	0.72224	0.6554	0.66416	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
55256	55256	SRR10204638	SRX6924593	SRS5455470	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 4 days post optic nerve crush replicate 2	Gene expression Danio rerio adult retina 4 days post optic nerve crush replicate 2	Drerio 4dpi retina RNA 2	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 4 dpi bio rep 2\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 4 days post optic nerve crush replicate 2	Drerio UWM RGC 4RNA2	Drerio UWM RGC 4RNA2	RNA was extracted and purified from retinas dissected from adult fish 4 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	4RNA2_R1.fastq.gz 4RNA2_R2.fastq.gz	fastq fastq	7484140350.0	73373925.0	4RNA2 R1.fastq.gz	0:51 1:51	A:2126190339;C:1593264319;G:1592780392;T:2159297230;N:12608070	51	51	2126190339	1593264319	1592780392	2159297230	12608070	SRX6924593	SRS5455470	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.92511	0.93129	0.18676	0.18654	0.71463	0.7162	0.63527	0.63752	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
55257	55257	SRR10204639	SRX6924592	SRS5455469	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 4 days post optic nerve crush replicate 1	Gene expression Danio rerio adult retina 4 days post optic nerve crush replicate 1	Drerio 4dpi retina RNA 1	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 4 dpi bio rep 1\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 4 days post optic nerve crush replicate 1	Drerio UWM RGC 4RNA1	Drerio UWM RGC 4RNA1	RNA was extracted and purified from retinas dissected from adult fish 4 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	4RNA1_R1.fastq.gz 4RNA1_R2.fastq.gz	fastq fastq	6935061294.0	67990797.0	4RNA1 R1.fastq.gz	0:51 1:51	A:1964630386;C:1485824393;G:1480949857;T:1992028352;N:11628306	51	51	1964630386	1485824393	1480949857	1992028352	11628306	SRX6924592	SRS5455469	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.93453	0.94014	0.1722	0.17026	0.73572	0.73827	0.69028	0.69543	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
55258	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
55259	55259	SRR10204642	SRX6924589	SRS5455466	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 2	Gene expression Danio rerio adult retina 2 days post optic nerve crush replicate 2	Drerio 2dpi retina RNA 2	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 2 dpi bio rep 2\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 2 days post optic nerve crush replicate 2	Drerio UWM RGC 2RNA2	Drerio UWM RGC 2RNA2	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	2RNA2_R2.fastq.gz 2RNA2_R1.fastq.gz	fastq fastq	6977471772.0	68406586.0	2RNA2 R1.fastq.gz	0:51 1:51	A:1981995190;C:1489959821;G:1484149460;T:2009613353;N:11753948	51	51	1981995190	1489959821	1484149460	2009613353	11753948	SRX6924589	SRS5455466	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.93385	0.93997	0.19069	0.19015	0.73651	0.73835	0.68081	0.68653	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
55260	55260	SRR10204643	SRX6924588	SRS5455465	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 1	Gene expression Danio rerio adult retina 2 days post optic nerve crush replicate 1	Drerio 2dpi retina RNA 1	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:regenerating adult retina 2 dpi bio rep 1\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina 2 days post optic nerve crush replicate 1	Drerio UWM RGC 2RNA1	Drerio UWM RGC 2RNA1	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	2RNA1_R2.fastq.gz 2RNA1_R1.fastq.gz	fastq fastq	6469582968.0	63427284.0	2RNA1 R1.fastq.gz	0:51 1:51	A:1813157686;C:1400431693;G:1399951469;T:1845208000;N:10834120	51	51	1813157686	1400431693	1399951469	1845208000	10834120	SRX6924588	SRS5455465	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.93131	0.93671	0.19698	0.19762	0.72352	0.72535	0.64821	0.66128	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
55261	55261	SRR10204644	SRX6924587	SRS5455464	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 control replicate 3	Gene expression Danio rerio adult retina control replicate 3	Drerio naive retina RNA 3	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:naive adult retina bio rep 3\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina control replicate 3	Drerio UWM RGC 0RNA3	Drerio UWM RGC 0RNA3	RNA was extracted and purified from retinas dissected from nave adult fish. 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	0RNA3_R2.fastq.gz 0RNA3_R1.fastq.gz	fastq fastq	6694261122.0	65630011.0	0RNA3 R1.fastq.gz	0:51 1:51	A:1891566170;C:1435251636;G:1433493916;T:1922724577;N:11224823	51	51	1891566170	1435251636	1433493916	1922724577	11224823	SRX6924587	SRS5455464	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.93273	0.93861	0.18459	0.18186	0.72904	0.72973	0.65489	0.66139	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
55262	55262	SRR10204645	SRX6924586	SRS5455463	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 control replicate 2	Gene expression Danio rerio adult retina control replicate 2	Drerio naive retina RNA 2	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:naive adult retina bio rep 2\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina control replicate 2	Drerio UWM RGC 0RNA2	Drerio UWM RGC 0RNA2	RNA was extracted and purified from retinas dissected from nave adult fish. 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	0RNA2_R1.fastq.gz 0RNA2_R2.fastq.gz	fastq fastq	6513990606.0	63862653.0	0RNA2 R1.fastq.gz	0:51 1:51	A:1825786240;C:1410546971;G:1411394242;T:1855285651;N:10977502	51	51	1825786240	1410546971	1411394242	1855285651	10977502	SRX6924586	SRS5455463	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.93459	0.94	0.1832	0.18225	0.73454	0.73555	0.64252	0.66283	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
55263	55263	SRR10204646	SRX6924585	SRS5455462	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 control replicate 1	Gene expression Danio rerio adult retina control replicate 1	Drerio naive retina RNA 1	strain:fgap43:egfp\|age:adult 7 month 9 month\|sex:mixed\|tissue:naive adult retina bio rep 1\|BioSampleModel:Model organism or animal	Gene expression Danio rerio adult retina control replicate 1	Drerio UWM RGC 0RNA1	Drerio UWM RGC 0RNA1	RNA was extracted and purified from retinas dissected from nave adult fish. 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	0RNA1_R1.fastq.gz 0RNA1_R2.fastq.gz	fastq fastq	6391207392.0	62658896.0	0RNA1 R1.fastq.gz	0:51 1:51	A:1784722513;C:1390855784;G:1392113360;T:1812817776;N:10697959	51	51	1784722513	1390855784	1392113360	1812817776	10697959	SRX6924585	SRS5455462	SRA970049	University of Wisconsin Milwaukee\|Biological Sciences	University of Wisconsin Milwaukee	2	0.93682	0.94308	0.18016	0.18105	0.74791	0.75006	0.64914	0.67416	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

Advanced export

JSON shape: default, array, newline-delimited

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;