metadata: run_metadata: 131 rows where devstage_curation_coarse = "Multi-stage" and tissue

131 rows where devstage_curation_coarse = "Multi-stage" and tissue_curation = "Eye"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.study_ref	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.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
33202	33202	SRR29848463	SRX25346228	SRS22013442	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	IPP 120hpf eye replicate4	GSM8399280	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf\|geo loc name:missing\|collection date:missing	IPP 120hpf eye replicate4	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf	GSM8399280	GSM8399280: IPP 120hpf eye replicate4; Danio rerio; RNA Seq	GSM8399280 r1	GSM8399280	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		IPP_eye_4_1.fq.gz IPP_eye_4_2.fq.gz	fastq fastq	7072359000.0	23574530.0	GSM8399280 r1	0:150 1:150	A:1896065137;C:1651795911;G:1640296836;T:1877949054;N:6252062	150	150	1896065137	1651795911	1640296836	1877949054	6252062	SRX25346228	SRS22013442	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.90538	0.89728	0.10331	0.10225	0.70593	0.70688	0.44853	0.44733	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33203	33203	SRR29848464	SRX25346227	SRS22013441	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	IPP 120hpf eye replicate3	GSM8399279	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf\|geo loc name:missing\|collection date:missing	IPP 120hpf eye replicate3	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf	GSM8399279	GSM8399279: IPP 120hpf eye replicate3; Danio rerio; RNA Seq	GSM8399279 r1	GSM8399279	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		IPP_eye_3_1.fq.gz IPP_eye_3_2.fq.gz	fastq fastq	6537519300.0	21791731.0	GSM8399279 r1	0:150 1:150	A:1760227857;C:1520738786;G:1507946481;T:1742862368;N:5743808	150	150	1760227857	1520738786	1507946481	1742862368	5743808	SRX25346227	SRS22013441	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.90945	0.90902	0.10894	0.10846	0.70431	0.7055	0.44535	0.43463	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33204	33204	SRR29848465	SRX25346226	SRS22013440	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	IPP 120hpf eye replicate2	GSM8399278	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf\|geo loc name:missing\|collection date:missing	IPP 120hpf eye replicate2	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf	GSM8399278	GSM8399278: IPP 120hpf eye replicate2; Danio rerio; RNA Seq	GSM8399278 r1	GSM8399278	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		IPP_eye_2_1.fq.gz IPP_eye_2_2.fq.gz	fastq fastq	7374435900.0	24581453.0	GSM8399278 r1	0:150 1:150	A:1986621253;C:1713862328;G:1699590477;T:1967874898;N:6486944	150	150	1986621253	1713862328	1699590477	1967874898	6486944	SRX25346226	SRS22013440	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.9091	0.90128	0.11122	0.1097	0.70201	0.70266	0.44395	0.4416	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33205	33205	SRR29848466	SRX25346225	SRS22013439	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	IPP 120hpf eye replicate1	GSM8399277	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf\|geo loc name:missing\|collection date:missing	IPP 120hpf eye replicate1	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:IPP\|time:120hpf	GSM8399277	GSM8399277: IPP 120hpf eye replicate1; Danio rerio; RNA Seq	GSM8399277 r1	GSM8399277	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		IPP_eye_1_1.fq.gz IPP_eye_1_2.fq.gz	fastq fastq	6538011600.0	21793372.0	GSM8399277 r1	0:150 1:150	A:1758764189;C:1520242338;G:1510361700;T:1742917780;N:5725593	150	150	1758764189	1520242338	1510361700	1742917780	5725593	SRX25346225	SRS22013439	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.91402	0.90585	0.11702	0.11558	0.70029	0.70094	0.45385	0.45435	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33206	33206	SRR29848467	SRX25346224	SRS22013438	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	DMSO 120hpf eye replicate4	GSM8399276	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf\|geo loc name:missing\|collection date:missing	DMSO 120hpf eye replicate4	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf	GSM8399276	GSM8399276: DMSO 120hpf eye replicate4; Danio rerio; RNA Seq	GSM8399276 r1	GSM8399276	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		Ctrl_eye_4_1.fq.gz Ctrl_eye_4_2.fq.gz	fastq fastq	7198057200.0	23993524.0	GSM8399276 r1	0:150 1:150	A:1929066670;C:1680279530;G:1672121671;T:1910263876;N:6325453	150	150	1929066670	1680279530	1672121671	1910263876	6325453	SRX25346224	SRS22013438	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.91947	0.90384	0.11309	0.11094	0.69576	0.69779	0.45803	0.45394	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33207	33207	SRR29848468	SRX25346223	SRS22013437	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	DMSO 120hpf eye replicate3	GSM8399275	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf\|geo loc name:missing\|collection date:missing	DMSO 120hpf eye replicate3	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf	GSM8399275	GSM8399275: DMSO 120hpf eye replicate3; Danio rerio; RNA Seq	GSM8399275 r1	GSM8399275	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		Ctrl_eye_3_1.fq.gz Ctrl_eye_3_2.fq.gz	fastq fastq	6349681200.0	21165604.0	GSM8399275 r1	0:150 1:150	A:1713020668;C:1474226584;G:1462505802;T:1694350186;N:5577960	150	150	1713020668	1474226584	1462505802	1694350186	5577960	SRX25346223	SRS22013437	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.89548	0.89606	0.09628	0.09664	0.71102	0.71161	0.44199	0.4354	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33208	33208	SRR29848469	SRX25346222	SRS22013436	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	DMSO 120hpf eye replicate2	GSM8399274	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf\|geo loc name:missing\|collection date:missing	DMSO 120hpf eye replicate2	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf	GSM8399274	GSM8399274: DMSO 120hpf eye replicate2; Danio rerio; RNA Seq	GSM8399274 r1	GSM8399274	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		Ctrl_eye_2_1.fq.gz Ctrl_eye_2_2.fq.gz	fastq fastq	6861299400.0	22870998.0	GSM8399274 r1	0:150 1:150	A:1839006136;C:1604484415;G:1591747628;T:1820307442;N:5753779	150	150	1839006136	1604484415	1591747628	1820307442	5753779	SRX25346222	SRS22013436	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.84164	0.83344	0.09914	0.09758	0.72034	0.72088	0.44273	0.4389	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33209	33209	SRR29848470	SRX25346221	SRS22013435	SRP520276	PRJNA1136505	Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish	GSE272355	Transcriptome Analysis	Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…	pubmed:39742644	DMSO 120hpf eye replicate1	GSM8399273	source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf\|geo loc name:missing\|collection date:missing	DMSO 120hpf eye replicate1	Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample	Dissected eye	Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification	Embryos were spawned and maintained in system water	tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf	GSM8399273	GSM8399273: DMSO 120hpf eye replicate1; Danio rerio; RNA Seq	GSM8399273 r1	GSM8399273	1	Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP520276		Ctrl_eye_1_1.fq.gz Ctrl_eye_1_2.fq.gz	fastq fastq	6544491000.0	21814970.0	GSM8399273 r1	0:150 1:150	A:1774622867;C:1510819173;G:1498655117;T:1754689449;N:5704394	150	150	1774622867	1510819173	1498655117	1754689449	5704394	SRX25346221	SRS22013435	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.86147	0.86095	0.11217	0.11159	0.71319	0.71352	0.44434	0.43886	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System
33274	33274	SRR29884407	SRX25380711	SRS22046064	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Male 5	GSM8406321	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Male 5	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406321	GSM8406321: Brain wh5 Male 5; Danio rerio; RNA Seq	GSM8406321 r1	GSM8406321	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample20KOMaleBrain_R1.fastq Sample20KOMaleBrain_R2.fastq	fastq fastq	5509276088.0	27917150.0	GSM8406321 r1	0:98.67 1:98.67	A:1498190193;C:1242495192;G:1267229536;T:1499431726;N:1929441	98	98	1498190193	1242495192	1267229536	1499431726	1929441	SRX25380711	SRS22046064	SRA1927371	Oregon State University	Oregon State University	2	0.94576	0.94515	0.14102	0.13871	0.69187	0.69077	0.52554	0.53007	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33275	33275	SRR29884408	SRX25380710	SRS22046063	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Male 4	GSM8406320	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Male 4	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406320	GSM8406320: Brain wh5 Male 4; Danio rerio; RNA Seq	GSM8406320 r1	GSM8406320	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample19KOMaleBrain_R1.fastq Sample19KOMaleBrain_R2.fastq	fastq fastq	6985356408.0	35379007.0	GSM8406320 r1	0:98.72 1:98.72	A:1889039547;C:1582622229;G:1620512342;T:1890746302;N:2435988	98	98	1889039547	1582622229	1620512342	1890746302	2435988	SRX25380710	SRS22046063	SRA1927371	Oregon State University	Oregon State University	2	0.94197	0.94411	0.14763	0.14597	0.69852	0.69826	0.54705	0.54822	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33276	33276	SRR29884409	SRX25380709	SRS22046062	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Male 3	GSM8406319	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Male 3	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406319	GSM8406319: Brain wh5 Male 3; Danio rerio; RNA Seq	GSM8406319 r1	GSM8406319	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample18KOMaleBrain_R1.fastq Sample18KOMaleBrain_R2.fastq	fastq fastq	5864072768.0	29837549.0	GSM8406319 r1	0:98.27 1:98.27	A:1609423180;C:1310248473;G:1328624911;T:1613750029;N:2026175	98	98	1609423180	1310248473	1328624911	1613750029	2026175	SRX25380709	SRS22046062	SRA1927371	Oregon State University	Oregon State University	2	0.94007	0.94233	0.14021	0.1386	0.69376	0.69317	0.51507	0.52214	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33277	33277	SRR29884410	SRX25380708	SRS22046061	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Male 2	GSM8406318	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Male 2	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406318	GSM8406318: Brain wh5 Male 2; Danio rerio; RNA Seq	GSM8406318 r1	GSM8406318	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample17KOMaleBrain_R1.fastq Sample17KOMaleBrain_R2.fastq	fastq fastq	5841328432.0	29860768.0	GSM8406318 r1	0:97.81 1:97.81	A:1606036785;C:1302920703;G:1321021765;T:1609306125;N:2043054	97	97	1606036785	1302920703	1321021765	1609306125	2043054	SRX25380708	SRS22046061	SRA1927371	Oregon State University	Oregon State University	2	0.9429	0.94295	0.14247	0.14023	0.69808	0.69739	0.51804	0.51798	69	69	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33278	33278	SRR29884411	SRX25380707	SRS22046060	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Male 1	GSM8406317	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Male 1	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406317	GSM8406317: Brain wh5 Male 1; Danio rerio; RNA Seq	GSM8406317 r1	GSM8406317	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample16KOMaleBrain_R1.fastq Sample16KOMaleBrain_R2.fastq	fastq fastq	6061816166.0	30929476.0	GSM8406317 r1	0:97.99 1:97.99	A:1666435568;C:1352308656;G:1373281492;T:1667671946;N:2118504	97	97	1666435568	1352308656	1373281492	1667671946	2118504	SRX25380707	SRS22046060	SRA1927371	Oregon State University	Oregon State University	2	0.94198	0.9434	0.14745	0.14621	0.69201	0.69138	0.52388	0.52247	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33279	33279	SRR29884412	SRX25380706	SRS22046059	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Female 5	GSM8406316	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Female 5	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406316	GSM8406316: Brain wh5 Female 5; Danio rerio; RNA Seq	GSM8406316 r1	GSM8406316	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample15KOFemaleBrain_R1.fastq Sample15KOFemaleBrain_R2.fastq	fastq fastq	5830172008.0	29715950.0	GSM8406316 r1	0:98.10 1:98.10	A:1585225847;C:1316585087;G:1339955604;T:1586384657;N:2020813	98	98	1585225847	1316585087	1339955604	1586384657	2020813	SRX25380706	SRS22046059	SRA1927371	Oregon State University	Oregon State University	2	0.94307	0.94571	0.13598	0.13423	0.69341	0.69309	0.52103	0.50706	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33280	33280	SRR29884413	SRX25380705	SRS22046058	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Female 4	GSM8406315	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Female 4	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406315	GSM8406315: Brain wh5 Female 4; Danio rerio; RNA Seq	GSM8406315 r1	GSM8406315	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample14KOFemaleBrain_R1.fastq Sample14KOFemaleBrain_R2.fastq	fastq fastq	6700791892.0	34096304.0	GSM8406315 r1	0:98.26 1:98.26	A:1817874372;C:1516000049;G:1546573687;T:1818017657;N:2326127	98	98	1817874372	1516000049	1546573687	1818017657	2326127	SRX25380705	SRS22046058	SRA1927371	Oregon State University	Oregon State University	2	0.94342	0.94623	0.13719	0.13523	0.69313	0.69254	0.53293	0.53816	84	84	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33281	33281	SRR29884414	SRX25380704	SRS22046057	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Female 3	GSM8406314	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Female 3	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406314	GSM8406314: Brain wh5 Female 3; Danio rerio; RNA Seq	GSM8406314 r1	GSM8406314	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample13KOFemaleBrain_R2.fastq Sample13KOFemaleBrain_R1.fastq	fastq fastq	6308152444.0	32040291.0	GSM8406314 r1	0:98.44 1:98.44	A:1698706705;C:1436132175;G:1472501608;T:1698611730;N:2200226	98	98	1698706705	1436132175	1472501608	1698611730	2200226	SRX25380704	SRS22046057	SRA1927371	Oregon State University	Oregon State University	2	0.94654	0.94476	0.1362	0.13304	0.694	0.69321	0.54515	0.53479	91	91	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33282	33282	SRR29884415	SRX25380703	SRS22046056	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Female 2	GSM8406313	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Female 2	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406313	GSM8406313: Brain wh5 Female 2; Danio rerio; RNA Seq	GSM8406313 r1	GSM8406313	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample12KOFemaleBrain_R1.fastq Sample12KOFemaleBrain_R2.fastq	fastq fastq	6503673262.0	33197897.0	GSM8406313 r1	0:97.95 1:97.95	A:1781196226;C:1457467194;G:1479672271;T:1783090598;N:2246973	97	97	1781196226	1457467194	1479672271	1783090598	2246973	SRX25380703	SRS22046056	SRA1927371	Oregon State University	Oregon State University	2	0.94227	0.94462	0.13793	0.13614	0.69359	0.69355	0.52971	0.52982	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33283	33283	SRR29884416	SRX25380702	SRS22046055	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain wh5 Female 1	GSM8406312	source name:eye\|tissue:eye\|genotype:wh5\|geo loc name:missing\|collection date:missing	Brain wh5 Female 1	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:wh5	GSM8406312	GSM8406312: Brain wh5 Female 1; Danio rerio; RNA Seq	GSM8406312 r1	GSM8406312	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample11KOFemaleBrain_R1.fastq Sample11KOFemaleBrain_R2.fastq	fastq fastq	5803578222.0	29408217.0	GSM8406312 r1	0:98.67 1:98.67	A:1586553028;C:1303184285;G:1323602566;T:1588219875;N:2018468	98	98	1586553028	1303184285	1323602566	1588219875	2018468	SRX25380702	SRS22046055	SRA1927371	Oregon State University	Oregon State University	2	0.94183	0.94513	0.1442	0.14286	0.6942	0.6942	0.51627	0.51673	93	93	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33284	33284	SRR29884417	SRX25380701	SRS22046053	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Male 5	GSM8406311	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Male 5	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406311	GSM8406311: Brain WT Male 5; Danio rerio; RNA Seq	GSM8406311 r1	GSM8406311	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample10WTMaleBrain_R1.fastq Sample10WTMaleBrain_R2.fastq	fastq fastq	4558024898.0	24051338.0	GSM8406311 r1	0:94.76 1:94.76	A:1220269093;C:1048518583;G:1068311203;T:1219299559;N:1626460	94	94	1220269093	1048518583	1068311203	1219299559	1626460	SRX25380701	SRS22046053	SRA1927371	Oregon State University	Oregon State University	2	0.93188	0.93167	0.1413	0.13958	0.70814	0.70875	0.52962	0.53051	80	80	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33285	33285	SRR29884418	SRX25380700	SRS22046052	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Male 4	GSM8406310	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Male 4	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406310	GSM8406310: Brain WT Male 4; Danio rerio; RNA Seq	GSM8406310 r1	GSM8406310	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample9WTMaleBrain_R1.fastq Sample9WTMaleBrain_R2.fastq	fastq fastq	5130577372.0	26157026.0	GSM8406310 r1	0:98.07 1:98.07	A:1409899035;C:1143333235;G:1163465644;T:1412102322;N:1777136	98	98	1409899035	1143333235	1163465644	1412102322	1777136	SRX25380700	SRS22046052	SRA1927371	Oregon State University	Oregon State University	2	0.94388	0.94533	0.13794	0.13603	0.69907	0.69867	0.52585	0.51928	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33286	33286	SRR29884419	SRX25380699	SRS22046054	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Male 3	GSM8406309	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Male 3	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406309	GSM8406309: Brain WT Male 3; Danio rerio; RNA Seq	GSM8406309 r1	GSM8406309	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample8WTMaleBrain_R1.fastq Sample8WTMaleBrain_R2.fastq	fastq fastq	7972815402.0	40447690.0	GSM8406309 r1	0:98.56 1:98.56	A:2168632819;C:1797135023;G:1834247957;T:2170022014;N:2777589	98	98	2168632819	1797135023	1834247957	2170022014	2777589	SRX25380699	SRS22046054	SRA1927371	Oregon State University	Oregon State University	2	0.94357	0.94705	0.13542	0.13436	0.69915	0.69863	0.52491	0.53063	81	81	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33287	33287	SRR29884420	SRX25380698	SRS22046051	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Male 2	GSM8406308	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Male 2	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406308	GSM8406308: Brain WT Male 2; Danio rerio; RNA Seq	GSM8406308 r1	GSM8406308	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample7WTMaleBrain_R1.fastq Sample7WTMaleBrain_R2.fastq	fastq fastq	7049713238.0	35734267.0	GSM8406308 r1	0:98.64 1:98.64	A:1906626428;C:1601451933;G:1627879106;T:1911302856;N:2452915	98	98	1906626428	1601451933	1627879106	1911302856	2452915	SRX25380698	SRS22046051	SRA1927371	Oregon State University	Oregon State University	2	0.9436	0.94611	0.15189	0.14982	0.70272	0.70293	0.54976	0.55028	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33288	33288	SRR29884421	SRX25380697	SRS22046050	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Male 1	GSM8406307	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Male 1	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406307	GSM8406307: Brain WT Male 1; Danio rerio; RNA Seq	GSM8406307 r1	GSM8406307	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample6WTMaleBrain_R1.fastq Sample6WTMaleBrain_R2.fastq	fastq fastq	5957369076.0	30406342.0	GSM8406307 r1	0:97.96 1:97.96	A:1609314070;C:1357455510;G:1376051649;T:1612447643;N:2100204	97	97	1609314070	1357455510	1376051649	1612447643	2100204	SRX25380697	SRS22046050	SRA1927371	Oregon State University	Oregon State University	2	0.94515	0.94596	0.13859	0.13741	0.69459	0.69386	0.5113	0.50829	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33289	33289	SRR29884422	SRX25380696	SRS22046048	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Female 5	GSM8406306	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Female 5	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406306	GSM8406306: Brain WT Female 5; Danio rerio; RNA Seq	GSM8406306 r1	GSM8406306	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample5WTFemaleBrain_R1.fastq Sample5WTFemaleBrain_R2.fastq	fastq fastq	6253800764.0	31754862.0	GSM8406306 r1	0:98.47 1:98.47	A:1706349321;C:1408396210;G:1425535859;T:1711348232;N:2171142	98	98	1706349321	1408396210	1425535859	1711348232	2171142	SRX25380696	SRS22046048	SRA1927371	Oregon State University	Oregon State University	2	0.94054	0.9433	0.13645	0.13468	0.69351	0.69268	0.50849	0.50886	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33290	33290	SRR29884423	SRX25380695	SRS22046047	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Female 4	GSM8406305	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Female 4	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406305	GSM8406305: Brain WT Female 4; Danio rerio; RNA Seq	GSM8406305 r1	GSM8406305	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample4WTFemaleBrain_R1.fastq Sample4WTFemaleBrain_R2.fastq	fastq fastq	6326747176.0	32181924.0	GSM8406305 r1	0:98.30 1:98.30	A:1726705163;C:1423533467;G:1441282364;T:1733022638;N:2203544	98	98	1726705163	1423533467	1441282364	1733022638	2203544	SRX25380695	SRS22046047	SRA1927371	Oregon State University	Oregon State University	2	0.94564	0.9463	0.13279	0.13015	0.69329	0.69264	0.52131	0.52995	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33291	33291	SRR29884424	SRX25380694	SRS22046049	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Female 3	GSM8406304	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Female 3	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406304	GSM8406304: Brain WT Female 3; Danio rerio; RNA Seq	GSM8406304 r1	GSM8406304	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample3WTFemaleBrain_R1.fastq Sample3WTFemaleBrain_R2.fastq	fastq fastq	6158432042.0	31268580.0	GSM8406304 r1	0:98.48 1:98.48	A:1663143400;C:1401049481;G:1427904493;T:1664192587;N:2142081	98	98	1663143400	1401049481	1427904493	1664192587	2142081	SRX25380694	SRS22046049	SRA1927371	Oregon State University	Oregon State University	2	0.94243	0.94497	0.13191	0.13006	0.68454	0.68335	0.53268	0.53362	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33292	33292	SRR29884425	SRX25380693	SRS22046046	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Female 2	GSM8406303	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Female 2	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406303	GSM8406303: Brain WT Female 2; Danio rerio; RNA Seq	GSM8406303 r1	GSM8406303	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample2WTFemaleBrain_R1.fastq Sample2WTFemaleBrain_R2.fastq	fastq fastq	5029227086.0	25468404.0	GSM8406303 r1	0:98.73 1:98.73	A:1373457097;C:1129749557;G:1148614258;T:1375648797;N:1757377	98	98	1373457097	1129749557	1148614258	1375648797	1757377	SRX25380693	SRS22046046	SRA1927371	Oregon State University	Oregon State University	2	0.94244	0.94484	0.14143	0.13943	0.69414	0.69292	0.52985	0.53107	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
33293	33293	SRR29884426	SRX25380692	SRS22046045	SRP520852	PRJNA1137393	Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function	GSE272589	Transcriptome Analysis	Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.	pubmed:39890032	Brain WT Female 1	GSM8406302	source name:eye\|tissue:eye\|genotype:WT\|geo loc name:missing\|collection date:missing	Brain WT Female 1	quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ \|1\| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa…	eye		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		tissue:eye\|genotype:WT	GSM8406302	GSM8406302: Brain WT Female 1; Danio rerio; RNA Seq	GSM8406302 r1	GSM8406302	1	RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP520852		Sample1WTFemaleBrain_R1.fastq Sample1WTFemaleBrain_R2.fastq	fastq fastq	6137098342.0	31214791.0	GSM8406302 r1	0:98.30 1:98.30	A:1678153918;C:1372921889;G:1402049594;T:1681827427;N:2145514	98	98	1678153918	1372921889	1402049594	1681827427	2145514	SRX25380692	SRS22046045	SRA1927371	Oregon State University	Oregon State University	2	0.93905	0.94293	0.14999	0.14877	0.69376	0.69292	0.52265	0.5227	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-07-18	Undetermined	Multi-stage	Eye	Sensory System
34264	34264	SRR31620789	SRX26985240	SRS23451898	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	36hpf dmut replicate 2	GSM8666793	source name:eye\|tissue:eye\|age:36\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	36hpf dmut replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:tet2 / tet3 /	GSM8666793	GSM8666793: 36hpf dmut replicate 2; Danio rerio; RNA Seq	GSM8666793 r1	GSM8666793	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36-2_DMUT_Library_GRO2554A2_S5_L001_R1_001.fastq.gz 36-2_DMUT_Library_GRO2554A2_S5_L001_R2_001.fastq.gz	fastq fastq	78416374900.0	664545550.0	GSM8666793 r1	0:28 1:90	A:21577013150;C:17939516025;G:19237904562;T:19657905130;N:4036033	28	90	21577013150	17939516025	19237904562	19657905130	4036033	SRX26985240	SRS23451898	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34265	34265	SRR31620790	SRX26985239	SRS23451897	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	36hpf dmut replicate 1	GSM8666792	source name:eye\|tissue:eye\|age:36\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	36hpf dmut replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:tet2 / tet3 /	GSM8666792	GSM8666792: 36hpf dmut replicate 1; Danio rerio; RNA Seq	GSM8666792 r1	GSM8666792	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R1_001.fastq.gz 36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R2_001.fastq.gz	fastq fastq	59960371084.0	508138738.0	GSM8666792 r1	0:28 1:90	A:16529389286;C:13737763948;G:14793638663;T:14896546895;N:3032292	28	90	16529389286	13737763948	14793638663	14896546895	3032292	SRX26985239	SRS23451897	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34266	34266	SRR31620791	SRX26985238	SRS23451896	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	36hpf sibCTL replicate 2	GSM8666791	source name:eye\|tissue:eye\|age:36\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	36hpf sibCTL replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:sibCTL	GSM8666791	GSM8666791: 36hpf sibCTL replicate 2; Danio rerio; RNA Seq	GSM8666791 r1	GSM8666791	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36-2_CTL_Library_GRO2554A1_S1_L001_R1_001.fastq.gz 36-2_CTL_Library_GRO2554A1_S1_L001_R2_001.fastq.gz	fastq fastq	75169575046.0	637030297.0	GSM8666791 r1	0:28 1:90	A:20921408123;C:16872043260;G:18114737773;T:19257530991;N:3854899	28	90	20921408123	16872043260	18114737773	19257530991	3854899	SRX26985238	SRS23451896	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34267	34267	SRR31620792	SRX26985237	SRS23451894	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	36hpf sibCTL replicate 1	GSM8666790	source name:eye\|tissue:eye\|age:36\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	36hpf sibCTL replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:sibCTL	GSM8666790	GSM8666790: 36hpf sibCTL replicate 1; Danio rerio; RNA Seq	GSM8666790 r1	GSM8666790	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36_1CTL_LIBRARY_GRO2455A5_S4_L001_R1_001.fastq.gz 36_1CTL_LIBRARY_GRO2455A5_S4_L001_R2_001.fastq.gz	fastq fastq	70127226422.0	594298529.0	GSM8666790 r1	0:28 1:90	A:19313304121;C:16059894416;G:17310188720;T:17440239265;N:3599900	28	90	19313304121	16059894416	17310188720	17440239265	3599900	SRX26985237	SRS23451894	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34268	34268	SRR31620793	SRX26985236	SRS23451895	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	48hpf dmut replicate 2	GSM8666789	source name:eye\|tissue:eye\|age:48\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	48hpf dmut replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:tet2 / tet3 /	GSM8666789	GSM8666789: 48hpf dmut replicate 2; Danio rerio; RNA Seq	GSM8666789 r1	GSM8666789	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		D48_2_GRO1775A18_S13_L001_R1_001.fastq.gz D48_2_GRO1775A18_S13_L001_R2_001.fastq.gz	fastq fastq	49713593756.0	421301642.0	GSM8666789 r1	0:28 1:90	A:13764945916;C:11293471135;G:11713999638;T:12938678190;N:2498877	28	90	13764945916	11293471135	11713999638	12938678190	2498877	SRX26985236	SRS23451895	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34269	34269	SRR31620794	SRX26985235	SRS23451893	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	48hpf dmut replicate 1	GSM8666788	source name:eye\|tissue:eye\|age:48\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	48hpf dmut replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:tet2 / tet3 /	GSM8666788	GSM8666788: 48hpf dmut replicate 1; Danio rerio; RNA Seq	GSM8666788 r1	GSM8666788	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		D48_1_GRO1775A16_S6_L001_R1_001.fastq.gz D48_1_GRO1775A16_S6_L001_R2_001.fastq.gz	fastq fastq	61017340862.0	517096109.0	GSM8666788 r1	0:28 1:90	A:16897864299;C:13758942283;G:14653497314;T:15703925956;N:3111010	28	90	16897864299	13758942283	14653497314	15703925956	3111010	SRX26985235	SRS23451893	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34270	34270	SRR31620795	SRX26985234	SRS23451891	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	48hpf sibCTL replicate 2	GSM8666787	source name:eye\|tissue:eye\|age:48\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	48hpf sibCTL replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:sibCTL	GSM8666787	GSM8666787: 48hpf sibCTL replicate 2; Danio rerio; RNA Seq	GSM8666787 r1	GSM8666787	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		C48_2_GRO1775A17_S10_L001_R1_001.fastq.gz C48_2_GRO1775A17_S10_L001_R2_001.fastq.gz	fastq fastq	41617041928.0	352686796.0	GSM8666787 r1	0:28 1:90	A:11784184401;C:9157967637;G:9647105654;T:11025644618;N:2139618	28	90	11784184401	9157967637	9647105654	11025644618	2139618	SRX26985234	SRS23451891	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34271	34271	SRR31620796	SRX26985233	SRS23451892	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq	pubmed:39713311;pubmed:40140485	48hpf sibCTL replicate 1	GSM8666786	source name:eye\|tissue:eye\|age:48\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	48hpf sibCTL replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:sibCTL	GSM8666786	GSM8666786: 48hpf sibCTL replicate 1; Danio rerio; RNA Seq	GSM8666786 r1	GSM8666786	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		C48_1_GRO1775A15_S2_L001_R1_001.fastq.gz C48_1_GRO1775A15_S2_L001_R2_001.fastq.gz	fastq fastq	54112599182.0	458581349.0	GSM8666786 r1	0:28 1:90	A:15198773029;C:11981463118;G:12618365415;T:14311218195;N:2779425	28	90	15198773029	11981463118	12618365415	14311218195	2779425	SRX26985233	SRS23451892	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
42525	42525	SRR5687196	SRX2921961	SRS2287821	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPneg5 2	GSM2670727	tissue:Zebrafish retinal cells not rods\|cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GFPneg5 2	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal cells not rods	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GSM2670727	GSM2670727: GFPneg5 2; Danio rerio; RNA Seq	GSM2670727		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670727	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPnegaitive5set2_GTGAAA_L001_R1_001.fastq.gz GFPnegaitive5set2_GTGAAA_L001_R2_001.fastq.gz	fastq fastq	1952022216.0	3158612.0	GSM2670727 r1	0:309 1:309	A:607016523;C:396466091;G:392683679;T:555854857;N:1066	309	309	607016523	396466091	392683679	555854857	1066	SRX2921961	SRS2287821	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.68529	0.70068	0.12269	0.12678	0.84133	0.856	0.71177	0.82957	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
42526	42526	SRR5687195	SRX2921960	SRS2287820	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPneg2 2	GSM2670726	tissue:Zebrafish retinal cells not rods\|cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GFPneg2 2	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal cells not rods	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GSM2670726	GSM2670726: GFPneg2 2; Danio rerio; RNA Seq	GSM2670726		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670726	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPnegaitive2set2_ATTCCT_L001_R1_001.fastq.gz GFPnegaitive2set2_ATTCCT_L001_R2_001.fastq.gz	fastq fastq	1811912964.0	2931898.0	GSM2670726 r1	0:309 1:309	A:578442167;C:369836482;G:350128044;T:513498823;N:7448	309	309	578442167	369836482	350128044	513498823	7448	SRX2921960	SRS2287820	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.64969	0.66677	0.08798	0.08966	0.87984	0.88684	0.88277	0.87474	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
42527	42527	SRR5687194	SRX2921959	SRS2287818	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPneg2	GSM2670725	tissue:Zebrafish retinal cells not rods\|cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GFPneg2	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal cells not rods	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GSM2670725	GSM2670725: GFPneg2; Danio rerio; RNA Seq	GSM2670725		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670725	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPnegaitive2_CAGATC_L001_R1_001.fastq.gz GFPnegaitive2_CAGATC_L001_R2_001.fastq.gz	fastq fastq	1718976888.0	2781516.0	GSM2670725 r1	0:309 1:309	A:529099301;C:352155163;G:350456178;T:487264195;N:2051	309	309	529099301	352155163	350456178	487264195	2051	SRX2921959	SRS2287818	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.71906	0.72599	0.20211	0.20881	0.77761	0.79289	0.65883	0.66469	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
42528	42528	SRR5687193	SRX2921958	SRS2287817	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPneg1	GSM2670724	tissue:Zebrafish retinal cells not rods\|cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GFPneg1	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal cells not rods	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GSM2670724	GSM2670724: GFPneg1; Danio rerio; RNA Seq	GSM2670724		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670724	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPnegaitive1_CGATGT_L001_R1_001.fastq.gz GFPnegaitive1_CGATGT_L001_R2_001.fastq.gz	fastq fastq	2018776104.0	3266628.0	GSM2670724 r1	0:309 1:309	A:608896808;C:414729064;G:413070681;T:582077754;N:1797	309	309	608896808	414729064	413070681	582077754	1797	SRX2921958	SRS2287817	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.72164	0.72585	0.19987	0.20795	0.78196	0.80505	0.65069	0.64958	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
42529	42529	SRR5687192	SRX2921957	SRS2287816	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPpos5 2	GSM2670723	tissue:Zebrafish retinal rod photoreceptors\|cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GFPpos5 2	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal rod photoreceptors	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GSM2670723	GSM2670723: GFPpos5 2; Danio rerio; RNA Seq	GSM2670723		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670723	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPpositive5set2_GTCCGC_L001_R1_001.fastq.gz GFPpositive5set2_GTCCGC_L001_R2_001.fastq.gz	fastq fastq	1951035888.0	3157016.0	GSM2670723 r1	0:309 1:309	A:601202476;C:409815484;G:396381725;T:543631225;N:4978	309	309	601202476	409815484	396381725	543631225	4978	SRX2921957	SRS2287816	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.66385	0.68047	0.17016	0.1787	0.82327	0.83437	0.66766	0.66412	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
42530	42530	SRR5687191	SRX2921956	SRS2287815	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPpos2 2	GSM2670722	tissue:Zebrafish retinal rod photoreceptors\|cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GFPpos2 2	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal rod photoreceptors	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GSM2670722	GSM2670722: GFPpos2 2; Danio rerio; RNA Seq	GSM2670722		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670722	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPpositive2set2_ACTGAT_L001_R1_001.fastq.gz GFPpositive2set2_ACTGAT_L001_R2_001.fastq.gz	fastq fastq	1756145880.0	2841660.0	GSM2670722 r1	0:309 1:309	A:564701465;C:354907068;G:340547873;T:495986512;N:2962	309	309	564701465	354907068	340547873	495986512	2962	SRX2921956	SRS2287815	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.57879	0.59269	0.16217	0.16717	0.85516	0.86277	0.7228	0.72512	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
42531	42531	SRR5687190	SRX2921955	SRS2287814	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPpos2	GSM2670721	tissue:Zebrafish retinal rod photoreceptors\|cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GFPpos2	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal rod photoreceptors	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GSM2670721	GSM2670721: GFPpos2; Danio rerio; RNA Seq	GSM2670721		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670721	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPpositive2_CCGTCC_L001_R1_001.fastq.gz GFPpositive2_CCGTCC_L001_R2_001.fastq.gz	fastq fastq	1812864684.0	2933438.0	GSM2670721 r1	0:309 1:309	A:549595811;C:382846743;G:374776217;T:505641489;N:4424	309	309	549595811	382846743	374776217	505641489	4424	SRX2921955	SRS2287814	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.62676	0.64046	0.22945	0.24228	0.81268	0.82574	0.60502	0.60668	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
42532	42532	SRR5687189	SRX2921954	SRS2287813	SRP109268	PRJNA390613	Transcripts within Rod Photoreceptors of the Zebrafish Retina	GSE100062	Transcriptome Analysis	Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.	pubmed:29422031	GFPpos1	GSM2670720	tissue:Zebrafish retinal rod photoreceptors\|cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GFPpos1	Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation	Zebrafish retinal rod photoreceptors	Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 µm nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.	cell type:rod photoreceptors\|genotype/variation:XOPS:eGFP\|cell type:GFP+; FACS sorted rods	GSM2670720	GSM2670720: GFPpos1; Danio rerio; RNA Seq	GSM2670720		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.	GEO Accession:GSM2670720	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq	SRP109268		GFPpositive1_TGACCA_L001_R1_001.fastq.gz GFPpositive1_TGACCA_L001_R2_001.fastq.gz	fastq fastq	2150958270.0	3480515.0	GSM2670720 r1	0:309 1:309	A:654306402;C:442036224;G:437971529;T:616642033;N:2082	309	309	654306402	442036224	437971529	616642033	2082	SRX2921954	SRS2287813	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.65859	0.66368	0.295	0.31011	0.79324	0.81454	0.55325	0.5597	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System
43470	43470	SRR6888834	SRX3839384	SRS3086672	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 right eye Scar	GSM3065990	tissue:right eye single cells\|cas9 injection:protein\|FISH id:P2\|organ:right eye\|sorted plates:1	P2 right eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:protein\|FISH id:P2\|organ:right eye\|sorted plates:1	GSM3065990	GSM3065990: P2 right eye Scar; Danio rerio; RNA Seq	GSM3065990		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065990	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		P2-Eye-right-p01-Scar_R1.fastq.gz P2-Eye-right-p01-Scar_R2.fastq.gz	fastq fastq	39029616.0	257084.0	GSM3065990 r1	0:75.94 1:75.88	A:7556894;C:11070936;G:13942796;T:6447595;N:11395	75	75	7556894	11070936	13942796	6447595	11395	SRX3839384	SRS3086672	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00367	0.00526	0.00323	0.00449	0.9988	0.99813	0.31168	0.32231	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Eye	Sensory System
43471	43471	SRR6888833	SRX3839383	SRS3086669	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 left eye Scar	GSM3065989	tissue:left eye single cells\|cas9 injection:protein\|FISH id:P2\|organ:left eye\|sorted plates:1	P2 left eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:protein\|FISH id:P2\|organ:left eye\|sorted plates:1	GSM3065989	GSM3065989: P2 left eye Scar; Danio rerio; RNA Seq	GSM3065989		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065989	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		P2-Eye-left-p01-Scar_R2.fastq.gz P2-Eye-left-p01-Scar_R1.fastq.gz	fastq fastq	38948398.0	256405.0	GSM3065989 r1	0:75.98 1:75.92	A:7098142;C:11543244;G:14180784;T:6112258;N:13970	75	75	7098142	11543244	14180784	6112258	13970	SRX3839383	SRS3086669	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00055	0.00086	0.00048	0.00075	0.99979	0.99971	0.63636	0.375	75	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Eye	Sensory System
43554	43554	SRR6020372	SRX3171475	SRS2501283	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Trans	GSM2776970	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776970	GSM2776970: R3 right eye Trans; Danio rerio; RNA Seq	GSM2776970		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776970	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R3_right-eye_Trans_p01_R1.fastq.gz R3_right-eye_Trans_p01_R2.fastq.gz	fastq fastq	1232363344.0	8159367.0	GSM2776970 r1	0:75.57 1:75.47	A:358721828;C:215851348;G:306533357;T:351024145;N:232666	75	75	358721828	215851348	306533357	351024145	232666	SRX3171475	SRS2501283	SRA602108	GEO	AVO, Hubrecht Institue	2	0.03878	0.48751	0.02989	0.31199	0.9932	0.95678	0.49115	0.57852	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43555	43555	SRR6020373	SRX3171475	SRS2501283	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Trans	GSM2776970	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776970	GSM2776970: R3 right eye Trans; Danio rerio; RNA Seq	GSM2776970		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776970	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R3_right-eye_Trans_p02_R1.fastq.gz R3_right-eye_Trans_p02_R2.fastq.gz	fastq fastq	13506918357.0	89381621.0	GSM2776970 r2	0:75.55 1:75.57	A:4378616211;C:1844732259;G:3577317917;T:3703682555;N:2569415	75	75	4378616211	1844732259	3577317917	3703682555	2569415	SRX3171475	SRS2501283	SRA602108	GEO	AVO, Hubrecht Institue	2	0.13968	0.38495	0.10884	0.24752	0.99393	0.97179	0.42155	0.58172	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43556	43556	SRR6020370	SRX3171474	SRS2501284	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Scar	GSM2776969	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776969	GSM2776969: R3 right eye Scar; Danio rerio; RNA Seq	GSM2776969		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776969	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R3_right-eye_Scar_p01_R1.fastq.gz R3_right-eye_Scar_p01_R2.fastq.gz	fastq fastq	16402556.0	107973.0	GSM2776969 r1	0:75.98 1:75.94	A:2913035;C:4716394;G:6012715;T:2757706;N:2706	75	75	2913035	4716394	6012715	2757706	2706	SRX3171474	SRS2501284	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00031	0.00215	0.00027	0.00065	0.99995	0.99941	0.5	0.375	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43557	43557	SRR6020371	SRX3171474	SRS2501284	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Scar	GSM2776969	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776969	GSM2776969: R3 right eye Scar; Danio rerio; RNA Seq	GSM2776969		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776969	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R3_right-eye_Scar_p02_R1.fastq.gz R3_right-eye_Scar_p02_R2.fastq.gz	fastq fastq	9167189.0	60361.0	GSM2776969 r2	0:75.94 1:75.94	A:1738353;C:2524474;G:3359567;T:1542690;N:2105	75	75	1738353	2524474	3359567	1542690	2105	SRX3171474	SRS2501284	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00212	0.01274	0.00127	0.00362	0.99955	0.99815	0.27586	0.42201	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43558	43558	SRR6020369	SRX3171473	SRS2501282	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 left eye Scar	GSM2776968	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:left eye\|sorted plates:1	R3 left eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R3\|tissue:left eye\|sorted plates:1	GSM2776968	GSM2776968: R3 left eye Scar; Danio rerio; RNA Seq	GSM2776968		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776968	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R3_left-eye_Scar_p01_R1.fastq.gz R3_left-eye_Scar_p01_R2.fastq.gz	fastq fastq	3260057.0	21462.0	GSM2776968 r1	0:75.94 1:75.96	A:576368;C:943970;G:1229076;T:510377;N:266	75	75	576368	943970	1229076	510377	266	SRX3171473	SRS2501282	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00061	0.00925	0.0003	0.00287	0.99991	0.99947	0.5	0.62962	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43605	43605	SRR6020322	SRX3171463	SRS2501272	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R1 right eye Trans	GSM2776958	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:right eye\|sorted plates:1	R1 right eye Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R1\|tissue:right eye\|sorted plates:1	GSM2776958	GSM2776958: R1 right eye Trans; Danio rerio; RNA Seq	GSM2776958		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776958	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R1_right-eye_Trans_p01_R1.fastq.gz R1_right-eye_Trans_p01_R2.fastq.gz	fastq fastq	5130322003.0	34025983.0	GSM2776958 r1	0:75.43 1:75.35	A:1849671847;C:731930699;G:648670890;T:1898907330;N:1141237	75	75	1849671847	731930699	648670890	1898907330	1141237	SRX3171463	SRS2501272	SRA602108	GEO	AVO, Hubrecht Institue	2	0.2345	0.49487	0.17483	0.32246	0.9683	0.91938	0.50419	0.54579	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43606	43606	SRR6020321	SRX3171462	SRS2501271	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R1 right eye Scar	GSM2776957	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:right eye\|sorted plates:1	R1 right eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R1\|tissue:right eye\|sorted plates:1	GSM2776957	GSM2776957: R1 right eye Scar; Danio rerio; RNA Seq	GSM2776957		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776957	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R1_right-eye_Scar_p01_R1.fastq.gz R1_right-eye_Scar_p01_R2.fastq.gz	fastq fastq	51349725.0	338093.0	GSM2776957 r1	0:75.98 1:75.90	A:9493047;C:14848060;G:18750237;T:8248478;N:9903	75	75	9493047	14848060	18750237	8248478	9903	SRX3171462	SRS2501271	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00015	0.00029	0.00011	0.00021	0.99993	0.99985	0.66666	0.57142	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43611	43611	SRR6020315	SRX3171459	SRS2501268	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R1 left eye Trans	GSM2776954	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 left eye Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	GSM2776954	GSM2776954: R1 left eye Trans; Danio rerio; RNA Seq	GSM2776954		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776954	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R1_left-eye_Trans_p01_R1.fastq.gz R1_left-eye_Trans_p01_R2.fastq.gz	fastq fastq	1046170155.0	6918434.0	GSM2776954 r1	0:75.69 1:75.52	A:295576695;C:221931427;G:229805854;T:298632621;N:223558	75	75	295576695	221931427	229805854	298632621	223558	SRX3171459	SRS2501268	SRA602108	GEO	AVO, Hubrecht Institue	2	0.06872	0.17373	0.05659	0.12922	0.9833	0.95611	0.46872	0.54838	75	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43612	43612	SRR6020316	SRX3171459	SRS2501268	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R1 left eye Trans	GSM2776954	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 left eye Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	GSM2776954	GSM2776954: R1 left eye Trans; Danio rerio; RNA Seq	GSM2776954		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776954	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R1_left-eye_Trans_p02_R2.fastq.gz R1_left-eye_Trans_p02_R1.fastq.gz	fastq fastq	25047483725.0	165912644.0	GSM2776954 r2	0:75.59 1:75.38	A:6912192763;C:5496852975;G:6032128490;T:6600903816;N:5405681	75	75	6912192763	5496852975	6032128490	6600903816	5405681	SRX3171459	SRS2501268	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01804	0.04542	0.01535	0.03794	0.99492	0.98774	0.42283	0.45955	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43613	43613	SRR6020313	SRX3171458	SRS2501266	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R1 left eye Scar	GSM2776953	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 left eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	GSM2776953	GSM2776953: R1 left eye Scar; Danio rerio; RNA Seq	GSM2776953		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776953	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R1_left-eye_Scar_p01_R1.fastq.gz R1_left-eye_Scar_p01_R2.fastq.gz	fastq fastq	430346860.0	2834154.0	GSM2776953 r1	0:75.96 1:75.88	A:78839865;C:124580997;G:157976167;T:68821337;N:128494	75	75	78839865	124580997	157976167	68821337	128494	SRX3171458	SRS2501266	SRA602108	GEO	AVO, Hubrecht Institue	2	9e-05	1e-05	5e-05	0.0	0.99997	0.99997	0.0	0.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43614	43614	SRR6020314	SRX3171458	SRS2501266	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R1 left eye Scar	GSM2776953	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 left eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	GSM2776953	GSM2776953: R1 left eye Scar; Danio rerio; RNA Seq	GSM2776953		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776953	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		R1_left-eye_Scar_p02_R1.fastq.gz R1_left-eye_Scar_p02_R2.fastq.gz	fastq fastq	840951649.0	5536337.0	GSM2776953 r2	0:75.98 1:75.91	A:151508446;C:241728170;G:312991163;T:134635263;N:88607	75	75	151508446	241728170	312991163	134635263	88607	SRX3171458	SRS2501266	SRA602108	GEO	AVO, Hubrecht Institue	2	8e-05	3e-05	5e-05	0.0	0.99997	0.99993	0.0	0.33333	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43626	43626	SRR5961764	SRX3119875	SRS2454734	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P1 right eye Scars	GSM2752198	source name:right eye single cells\|cas9 injection:protein\|FISH id:P1\|tissue:right eye\|sorted plates:2	P1 right eye Scars	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:protein\|FISH id:P1\|tissue:right eye\|sorted plates:2	GSM2752198	GSM2752198: P1 right eye Scars; Danio rerio; RNA Seq	GSM2752198		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2752198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		P1_right-eye_Scar_p01_R1.fastq.gz P1_right-eye_Scar_p01_R2.fastq.gz	fastq fastq	41294204.0	271740.0	GSM2752198 r1	0:75.99 1:75.97	A:7444211;C:11950093;G:15212116;T:6685156;N:2628	75	75	7444211	11950093	15212116	6685156	2628	SRX3119875	SRS2454734	SRA602108	GEO	AVO, Hubrecht Institue	2	6e-05	0.00023	4e-05	0.00017	0.99993	0.99981	0.66666	0.66666	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-08-23	Undetermined	Multi-stage	Eye	Sensory System
43627	43627	SRR6930577	SRX3119875	SRS2454734	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P1 right eye Scars	GSM2752198	source name:right eye single cells\|cas9 injection:protein\|FISH id:P1\|tissue:right eye\|sorted plates:2	P1 right eye Scars	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern	right eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:protein\|FISH id:P1\|tissue:right eye\|sorted plates:2	GSM2752198	GSM2752198: P1 right eye Scars; Danio rerio; RNA Seq	GSM2752198		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2752198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		P1_right-eye_Scar_p02_R1.fastq.gz P1_right-eye_Scar_p02_R2.fastq.gz	fastq fastq	91033438.0	599208.0	GSM2752198 r2	0:75.97 1:75.96	A:16805120;C:25814395;G:33115601;T:15269609;N:28713	75	75	16805120	25814395	33115601	15269609	28713	SRX3119875	SRS2454734	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00381	0.00672	0.00333	0.00593	0.99845	0.9975	0.45238	0.50769	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-08-23	Undetermined	Multi-stage	Eye	Sensory System
43629	43629	SRR5961762	SRX3119873	SRS2454732	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P1 left eye Scars	GSM2752196	source name:left eye single cells\|cas9 injection:protein\|FISH id:P1\|tissue:left eye\|sorted plates:1	P1 left eye Scars	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern	left eye single cells		post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters		cas9 injection:protein\|FISH id:P1\|tissue:left eye\|sorted plates:1	GSM2752196	GSM2752196: P1 left eye Scars; Danio rerio; RNA Seq	GSM2752196		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2752196	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018		P1_left-eye_Scar_p01_R1.fastq.gz P1_left-eye_Scar_p01_R2.fastq.gz	fastq fastq	161576029.0	1063213.0	GSM2752196 r1	0:75.98 1:75.99	A:29049869;C:46414226;G:59509149;T:26592886;N:9899	75	75	29049869	46414226	59509149	26592886	9899	SRX3119873	SRS2454732	SRA602108	GEO	AVO, Hubrecht Institue	2	1e-05	2e-05	0.0	0.0	1.0	0.99995		0.5	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-08-23	Undetermined	Multi-stage	Eye	Sensory System
52168	52168	SRR18181438	SRX14328402	SRS12144033	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Eye3	GSM5924276	source name:eye\|strain:Tubingen\|tissue:eye\|genotype:wild type	Eye3	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	eye		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:eye\|genotype:wild type	GSM5924276	GSM5924276: Eye3; Danio rerio; RNA Seq	GSM5924276		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM5924276	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10\|intentional duplicate	Eye3.bam	bam	15432297300.0	51440991.0	GSM5924276 r1	0:150 1:150	A:4354553670;C:2433124600;G:2447610770;T:6195160523;N:1847737	150	150	4354553670	2433124600	2447610770	6195160523	1847737	SRX14328402	SRS12144033	SRA880843	GEO	Zhejiang University	2	5e-05	0.60307	4e-05	0.06123	1.0	0.86265		0.57125	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2022-03-01	Undetermined	Multi-stage	Eye	Sensory System
52190	52190	SRR9058957	SRX5835157	SRS4761453	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Eye1	GSM3768154	source name:eye\|strain:Tubingen\|genotype/variation:wild type\|tissue:eye	Eye1	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	eye		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype/variation:wild type\|tissue:eye	GSM3768154	GSM3768154: Eye1; Danio rerio; RNA Seq	GSM3768154		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3768154	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten	SRP194254	assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index	Eye1.bam	bam	37155841274.0	123032587.0	GSM3768154 r1	0:151 1:151	A:9138846228;C:6458258540;G:6507520861;T:15044585234;N:6630411	151	151	9138846228	6458258540	6507520861	15044585234	6630411	SRX5835157	SRS4761453	SRA880843	GEO	Zhejiang University	2	2e-05	0.84079	0.0	0.04869	0.99997	0.84167	0.0	0.66089	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-05-15	Undetermined	Multi-stage	Eye	Sensory System
52207	52207	SRR8991397	SRX5770465	SRS4704574	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Eye2	GSM3740950	source name:eye\|strain:Tubingen\|genotype:wild type\|tissue:eye	Eye2	The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	eye		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype:wild type\|tissue:eye	GSM3740950	GSM3740950: Eye2; Danio rerio; RNA Seq	GSM3740950		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3740950	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10	Eye2.bam	bam	37560825992.0	124373596.0	GSM3740950 r1	0:151 1:151	A:9124157397;C:6448456288;G:6525562883;T:15454078654;N:8570770	151	151	9124157397	6448456288	6525562883	15454078654	8570770	SRX5770465	SRS4704574	SRA880843	GEO	Zhejiang University	2	0.0	0.79235	0.0	0.0383	1.0	0.84981		0.57745	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-04-30	Undetermined	Multi-stage	Eye	Sensory System
53513	53513	SRR9906847	SRX6657804	SRS5218265	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahN36R2	GSM4007833	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 2	zfRNAnmdahN36R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 2	GSM4007833	GSM4007833: zfRNAnmdahN36R2; Danio rerio; RNA Seq	GSM4007833		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF4N_S8_R1_001.fastq.gz THoa-TF4N_S8_R2_001.fastq.gz	fastq fastq	7928700600.0	52858004.0	GSM4007833 r1	0:75 1:75	A:2214653986;C:1699850211;G:1809132429;T:2204054149;N:1009825	75	75	2214653986	1699850211	1809132429	2204054149	1009825	SRX6657804	SRS5218265	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.88014	0.90383	0.394	0.41783	0.76607	0.77043	0.5474	0.55256	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53514	53514	SRR9906846	SRX6657803	SRS5218264	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahN36R1	GSM4007832	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 1	zfRNAnmdahN36R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 1	GSM4007832	GSM4007832: zfRNAnmdahN36R1; Danio rerio; RNA Seq	GSM4007832		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF3N_S7_R1_001.fastq.gz THoa-TF3N_S7_R2_001.fastq.gz	fastq fastq	7863596250.0	52423975.0	GSM4007832 r1	0:75 1:75	A:2245214380;C:1641445245;G:1740385747;T:2235554179;N:996699	75	75	2245214380	1641445245	1740385747	2235554179	996699	SRX6657803	SRS5218264	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.86899	0.89643	0.43639	0.46473	0.76631	0.77086	0.53259	0.53462	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53515	53515	SRR9906845	SRX6657802	SRS5218263	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahN20R2	GSM4007831	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 2	zfRNAnmdahN20R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 2	GSM4007831	GSM4007831: zfRNAnmdahN20R2; Danio rerio; RNA Seq	GSM4007831		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF2N_S6_R1_001.fastq.gz THoa-TF2N_S6_R2_001.fastq.gz	fastq fastq	11221029450.0	74806863.0	GSM4007831 r1	0:75 1:75	A:3206652122;C:2349148827;G:2475237997;T:3188565893;N:1424611	75	75	3206652122	2349148827	2475237997	3188565893	1424611	SRX6657802	SRS5218263	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.86571	0.89458	0.44089	0.4703	0.77163	0.77573	0.54887	0.54576	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53516	53516	SRR9906844	SRX6657801	SRS5218262	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahN20R1	GSM4007830	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 1	zfRNAnmdahN20R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 1	GSM4007830	GSM4007830: zfRNAnmdahN20R1; Danio rerio; RNA Seq	GSM4007830		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF1N_S5_R1_001.fastq.gz THoa-TF1N_S5_R2_001.fastq.gz	fastq fastq	11263633950.0	75090893.0	GSM4007830 r1	0:75 1:75	A:3198241763;C:2374935676;G:2514695492;T:3174314457;N:1446562	75	75	3198241763	2374935676	2514695492	3174314457	1446562	SRX6657801	SRS5218262	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.87624	0.90304	0.39909	0.42417	0.76984	0.77376	0.53406	0.53718	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53517	53517	SRR9906843	SRX6657800	SRS5218261	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahP36R2	GSM4007829	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 2	zfRNAnmdahP36R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 2	GSM4007829	GSM4007829: zfRNAnmdahP36R2; Danio rerio; RNA Seq	GSM4007829		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF4P_S4_R1_001.fastq.gz THoa-TF4P_S4_R2_001.fastq.gz	fastq fastq	10599378900.0	70662526.0	GSM4007829 r1	0:75 1:75	A:2917939167;C:2338922409;G:2472546084;T:2868616483;N:1354757	75	75	2917939167	2338922409	2472546084	2868616483	1354757	SRX6657800	SRS5218261	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.89693	0.9159	0.31259	0.33022	0.7371	0.74182	0.56412	0.56559	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53518	53518	SRR9906842	SRX6657799	SRS5218260	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahP36R1	GSM4007828	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 1	zfRNAnmdahP36R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 1	GSM4007828	GSM4007828: zfRNAnmdahP36R1; Danio rerio; RNA Seq	GSM4007828		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF3P_S3_R1_001.fastq.gz THoa-TF3P_S3_R2_001.fastq.gz	fastq fastq	11034687150.0	73564581.0	GSM4007828 r1	0:75 1:75	A:2954740084;C:2509220120;G:2662792371;T:2906521814;N:1412761	75	75	2954740084	2509220120	2662792371	2906521814	1412761	SRX6657799	SRS5218260	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.90866	0.9253	0.29649	0.3138	0.7419	0.74793	0.57845	0.59013	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53519	53519	SRR9906841	SRX6657798	SRS5218259	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahP20R2	GSM4007827	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	zfRNAnmdahP20R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	GSM4007827	GSM4007827: zfRNAnmdahP20R2; Danio rerio; RNA Seq	GSM4007827		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF2P_S2_R1_001.fastq.gz THoa-TF2P_S2_R2_001.fastq.gz	fastq fastq	10416796950.0	69445313.0	GSM4007827 r1	0:75 1:75	A:2846027907;C:2324721617;G:2438862539;T:2805866203;N:1318684	75	75	2846027907	2324721617	2438862539	2805866203	1318684	SRX6657798	SRS5218259	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.89999	0.92352	0.30772	0.32822	0.74823	0.75089	0.5489	0.55828	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53520	53520	SRR9906840	SRX6657797	SRS5218258	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdahP20R1	GSM4007826	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 1	zfRNAnmdahP20R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 1	GSM4007826	GSM4007826: zfRNAnmdahP20R1; Danio rerio; RNA Seq	GSM4007826		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-TF1P_S1_R1_001.fastq.gz THoa-TF1P_S1_R2_001.fastq.gz	fastq fastq	11087990850.0	73919939.0	GSM4007826 r1	0:75 1:75	A:3086331907;C:2414289581;G:2547013161;T:3038947630;N:1408571	75	75	3086331907	2414289581	2547013161	3038947630	1408571	SRX6657797	SRS5218258	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.89541	0.9175	0.30129	0.32289	0.7417	0.74714	0.55292	0.55122	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53521	53521	SRR9906839	SRX6657796	SRS5218257	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN36R2	GSM4007825	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 2	zfRNAnmdaN36R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 2	GSM4007825	GSM4007825: zfRNAnmdaN36R2; Danio rerio; RNA Seq	GSM4007825		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF16N_S7_R1_001.fastq.gz THoa-DF16N_S7_R2_001.fastq.gz	fastq fastq	7593295650.0	50621971.0	GSM4007825 r1	0:75 1:75	A:1842742463;C:1931868500;G:2009769570;T:1805690959;N:3224158	75	75	1842742463	1931868500	2009769570	1805690959	3224158	SRX6657796	SRS5218257	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93981	0.95204	0.24731	0.26265	0.81412	0.81811	0.67154	0.67196	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53522	53522	SRR9906838	SRX6657795	SRS5218256	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN36R1	GSM4007824	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 1	zfRNAnmdaN36R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 1	GSM4007824	GSM4007824: zfRNAnmdaN36R1; Danio rerio; RNA Seq	GSM4007824		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF15N_S6_R1_001.fastq.gz THoa-DF15N_S6_R2_001.fastq.gz	fastq fastq	7927875450.0	52852503.0	GSM4007824 r1	0:75 1:75	A:1938512738;C:1988054202;G:2080463145;T:1917497438;N:3347927	75	75	1938512738	1988054202	2080463145	1917497438	3347927	SRX6657795	SRS5218256	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93468	0.94808	0.25462	0.27334	0.81262	0.81548	0.6351	0.66108	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53523	53523	SRR9906837	SRX6657794	SRS5218255	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN20R2	GSM4007823	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 2	zfRNAnmdaN20R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 2	GSM4007823	GSM4007823: zfRNAnmdaN20R2; Danio rerio; RNA Seq	GSM4007823		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		DF29N_S7_R1_001.fastq.gz DF29N_S7_R2_001.fastq.gz	fastq fastq	7876840694.0	52829905.0	GSM4007823 r1	0:74.55 1:74.55	A:2010274884;C:1895760244;G:1963812981;T:2004863879;N:2128706	74	74	2010274884	1895760244	1963812981	2004863879	2128706	SRX6657794	SRS5218255	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.90858	0.91979	0.28522	0.29978	0.81742	0.82104	0.6582	0.65941	74	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53524	53524	SRR9906836	SRX6657793	SRS5218254	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN20R1	GSM4007822	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 1	zfRNAnmdaN20R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 1	GSM4007822	GSM4007822: zfRNAnmdaN20R1; Danio rerio; RNA Seq	GSM4007822		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF13N_S5_R1_001.fastq.gz THoa-DF13N_S5_R2_001.fastq.gz	fastq fastq	8003905950.0	53359373.0	GSM4007822 r1	0:75 1:75	A:1925414212;C:2030985118;G:2137411382;T:1906727349;N:3367889	75	75	1925414212	2030985118	2137411382	1906727349	3367889	SRX6657793	SRS5218254	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.94476	0.95272	0.22584	0.24304	0.81404	0.8186	0.68349	0.6811	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53525	53525	SRR9906835	SRX6657792	SRS5218253	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN10R2	GSM4007821	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 2	zfRNAnmdaN10R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 2	GSM4007821	GSM4007821: zfRNAnmdaN10R2; Danio rerio; RNA Seq	GSM4007821		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF12N_S4_R1_001.fastq.gz THoa-DF12N_S4_R2_001.fastq.gz	fastq fastq	7571445300.0	50476302.0	GSM4007821 r1	0:75 1:75	A:1961355978;C:1793618129;G:1874282399;T:1938980874;N:3207920	75	75	1961355978	1793618129	1874282399	1938980874	3207920	SRX6657792	SRS5218253	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.91789	0.93655	0.28528	0.30489	0.7989	0.80079	0.6136	0.62523	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53526	53526	SRR9906834	SRX6657791	SRS5218252	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN10R1	GSM4007820	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 1	zfRNAnmdaN10R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 1	GSM4007820	GSM4007820: zfRNAnmdaN10R1; Danio rerio; RNA Seq	GSM4007820		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF11N_S3_R1_001.fastq.gz THoa-DF11N_S3_R2_001.fastq.gz	fastq fastq	6515556150.0	43437041.0	GSM4007820 r1	0:75 1:75	A:1542198255;C:1688374350;G:1771407578;T:1510810367;N:2765600	75	75	1542198255	1688374350	1771407578	1510810367	2765600	SRX6657791	SRS5218252	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.94732	0.95644	0.21363	0.23778	0.82698	0.83019	0.69676	0.69466	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53527	53527	SRR9906833	SRX6657790	SRS5218251	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN04R2	GSM4007819	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 2	zfRNAnmdaN04R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 2	GSM4007819	GSM4007819: zfRNAnmdaN04R2; Danio rerio; RNA Seq	GSM4007819		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF10N_S2_R1_001.fastq.gz THoa-DF10N_S2_R2_001.fastq.gz	fastq fastq	7522510200.0	50150068.0	GSM4007819 r1	0:75 1:75	A:1828130590;C:1927363004;G:1976726604;T:1787097599;N:3192403	75	75	1828130590	1927363004	1976726604	1787097599	3192403	SRX6657790	SRS5218251	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.94502	0.9468	0.20905	0.22188	0.8436	0.8454	0.72316	0.72635	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53528	53528	SRR9906832	SRX6657789	SRS5218250	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaN04R1	GSM4007818	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 1	zfRNAnmdaN04R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 1	GSM4007818	GSM4007818: zfRNAnmdaN04R1; Danio rerio; RNA Seq	GSM4007818		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF9N_S1_R1_001.fastq.gz THoa-DF9N_S1_R2_001.fastq.gz	fastq fastq	7392867750.0	49285785.0	GSM4007818 r1	0:75 1:75	A:1807364965;C:1871069705;G:1942445368;T:1768857698;N:3130014	75	75	1807364965	1871069705	1942445368	1768857698	3130014	SRX6657789	SRS5218250	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93966	0.94358	0.23683	0.25285	0.81785	0.82012	0.67242	0.69507	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53529	53529	SRR9906831	SRX6657788	SRS5218249	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP36R2	GSM4007817	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 2	zfRNAnmdaP36R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 2	GSM4007817	GSM4007817: zfRNAnmdaP36R2; Danio rerio; RNA Seq	GSM4007817		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF16P_S7_R1_001.fastq.gz THoa-DF16P_S7_R2_001.fastq.gz	fastq fastq	6373735248.0	42722100.0	GSM4007817 r1	0:74.59 1:74.60	A:1515782870;C:1648277663;G:1705206622;T:1501843556;N:2624537	74	74	1515782870	1648277663	1705206622	1501843556	2624537	SRX6657788	SRS5218249	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.94124	0.94458	0.14833	0.15451	0.82012	0.8239	0.6622	0.67093	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53530	53530	SRR9906830	SRX6657787	SRS5218248	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP36R1	GSM4007816	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 1	zfRNAnmdaP36R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 1	GSM4007816	GSM4007816: zfRNAnmdaP36R1; Danio rerio; RNA Seq	GSM4007816		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF15P_S6_R1_001.fastq.gz THoa-DF15P_S6_R2_001.fastq.gz	fastq fastq	6569582369.0	44039507.0	GSM4007816 r1	0:74.58 1:74.59	A:1581167169;C:1668076484;G:1734283999;T:1583362809;N:2691908	74	74	1581167169	1668076484	1734283999	1583362809	2691908	SRX6657787	SRS5218248	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.92986	0.93029	0.15525	0.16583	0.80825	0.81172	0.65632	0.67275	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53531	53531	SRR9906829	SRX6657786	SRS5218247	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP20R2R2	GSM4007815	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	zfRNAnmdaP20R2R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	GSM4007815	GSM4007815: zfRNAnmdaP20R2R2; Danio rerio; RNA Seq	GSM4007815		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF29P-run2_S7_R1_001.fastq.gz THoa-DF29P-run2_S7_R2_001.fastq.gz	fastq fastq	4138950900.0	27593006.0	GSM4007815 r1	0:75 1:75	A:1036118589;C:1022903513;G:1048995320;T:1027851668;N:3081810	75	75	1036118589	1022903513	1048995320	1027851668	3081810	SRX6657786	SRS5218247	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.94004	0.94676	0.14485	0.14607	0.80986	0.8102	0.6594	0.60583	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53532	53532	SRR9906828	SRX6657785	SRS5218246	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP20R2R1	GSM4007814	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	zfRNAnmdaP20R2R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	GSM4007814	GSM4007814: zfRNAnmdaP20R2R1; Danio rerio; RNA Seq	GSM4007814		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF29P-run1_S7_R1_001.fastq.gz THoa-DF29P-run1_S7_R2_001.fastq.gz	fastq fastq	2345611650.0	15637411.0	GSM4007814 r1	0:75 1:75	A:586100477;C:579733712;G:596500443;T:582730098;N:546920	75	75	586100477	579733712	596500443	582730098	546920	SRX6657785	SRS5218246	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93951	0.94484	0.14437	0.14581	0.80738	0.80724	0.66526	0.58765	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53533	53533	SRR9906827	SRX6657784	SRS5218245	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP20R1	GSM4007813	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 1	zfRNAnmdaP20R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 1	GSM4007813	GSM4007813: zfRNAnmdaP20R1; Danio rerio; RNA Seq	GSM4007813		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF13P_S5_R1_001.fastq.gz THoa-DF13P_S5_R2_001.fastq.gz	fastq fastq	7039003072.0	47187560.0	GSM4007813 r1	0:74.58 1:74.59	A:1712945752;C:1757482359;G:1842953199;T:1722863594;N:2758168	74	74	1712945752	1757482359	1842953199	1722863594	2758168	SRX6657784	SRS5218245	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.94233	0.94816	0.14168	0.15153	0.79977	0.80549	0.62578	0.64305	72	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53534	53534	SRR9906826	SRX6657783	SRS5218244	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP10R2	GSM4007812	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:10hr\|replicate:Replicate 2	zfRNAnmdaP10R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:10hr\|replicate:Replicate 2	GSM4007812	GSM4007812: zfRNAnmdaP10R2; Danio rerio; RNA Seq	GSM4007812		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF12P_S4_R1_001.fastq.gz THoa-DF12P_S4_R2_001.fastq.gz	fastq fastq	5745697684.0	38525032.0	GSM4007812 r1	0:74.57 1:74.57	A:1416523959;C:1432155681;G:1476691642;T:1417880795;N:2445607	74	74	1416523959	1432155681	1476691642	1417880795	2445607	SRX6657783	SRS5218244	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93423	0.94349	0.1837	0.191	0.81146	0.81446	0.64969	0.65118	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53535	53535	SRR9906825	SRX6657782	SRS5218243	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP10R1	GSM4007811	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:10hr\|replicate:Replicate 1	zfRNAnmdaP10R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:10hr\|replicate:Replicate 1	GSM4007811	GSM4007811: zfRNAnmdaP10R1; Danio rerio; RNA Seq	GSM4007811		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF11P_S3_R1_001.fastq.gz THoa-DF11P_S3_R2_001.fastq.gz	fastq fastq	4687597951.0	31430998.0	GSM4007811 r1	0:74.56 1:74.58	A:1186920007;C:1133558971;G:1178442772;T:1186839573;N:1836628	74	74	1186920007	1133558971	1178442772	1186839573	1836628	SRX6657782	SRS5218243	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93636	0.94612	0.16988	0.17882	0.80014	0.80424	0.63955	0.63931	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53536	53536	SRR9906824	SRX6657781	SRS5218242	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP04R2	GSM4007810	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:4hr\|replicate:Replicate 2	zfRNAnmdaP04R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:4hr\|replicate:Replicate 2	GSM4007810	GSM4007810: zfRNAnmdaP04R2; Danio rerio; RNA Seq	GSM4007810		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF10P_S2_R1_001.fastq.gz THoa-DF10P_S2_R2_001.fastq.gz	fastq fastq	5482033611.0	36761528.0	GSM4007810 r1	0:74.56 1:74.57	A:1399163955;C:1327953597;G:1360796447;T:1391846223;N:2273389	74	74	1399163955	1327953597	1360796447	1391846223	2273389	SRX6657781	SRS5218242	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.86015	0.87027	0.18565	0.19683	0.83349	0.83666	0.62827	0.63846	72	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53537	53537	SRR9906823	SRX6657780	SRS5218241	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAnmdaP04R1	GSM4007809	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:4hr\|replicate:Replicate 1	zfRNAnmdaP04R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:GFP]mi2001 AB\|condition:NMDA treatment\|cell population of facs sorting:GFP+\|time:4hr\|replicate:Replicate 1	GSM4007809	GSM4007809: zfRNAnmdaP04R1; Danio rerio; RNA Seq	GSM4007809		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF9P_S1_R1_001.fastq.gz THoa-DF9P_S1_R2_001.fastq.gz	fastq fastq	21735411065.0	145822702.0	GSM4007809 r1	0:74.54 1:74.51	A:5770843248;C:4924186554;G:5223386393;T:5808415210;N:8579660	74	74	5770843248	4924186554	5223386393	5808415210	8579660	SRX6657780	SRS5218241	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.32804	0.332	0.08428	0.08869	0.87584	0.87969	0.63905	0.65793	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53538	53538	SRR9906822	SRX6657779	SRS5218240	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN36R2	GSM4007808	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 2	zfRNAldtN36R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 2	GSM4007808	GSM4007808: zfRNAldtN36R2; Danio rerio; RNA Seq	GSM4007808		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF8N_S9_R1_001.fastq.gz THoa-DF8N_S9_R2_001.fastq.gz	fastq fastq	7461557400.0	49743716.0	GSM4007808 r1	0:75 1:75	A:1829397197;C:1872660811;G:1943038567;T:1813306644;N:3154181	75	75	1829397197	1872660811	1943038567	1813306644	3154181	SRX6657779	SRS5218240	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.9181	0.93155	0.26114	0.27679	0.80152	0.8045	0.67335	0.67474	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53539	53539	SRR9906821	SRX6657778	SRS5218239	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN36R1	GSM4007807	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 1	zfRNAldtN36R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:36hr\|replicate:Replicate 1	GSM4007807	GSM4007807: zfRNAldtN36R1; Danio rerio; RNA Seq	GSM4007807		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF7N_S8_R1_001.fastq.gz THoa-DF7N_S8_R2_001.fastq.gz	fastq fastq	7310480700.0	48736538.0	GSM4007807 r1	0:75 1:75	A:1851060267;C:1761439990;G:1858394380;T:1836486630;N:3099433	75	75	1851060267	1761439990	1858394380	1836486630	3099433	SRX6657778	SRS5218239	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.92044	0.93499	0.28396	0.29825	0.77948	0.7825	0.62758	0.63403	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53540	53540	SRR9906820	SRX6657777	SRS5218238	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN20R2	GSM4007806	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 2	zfRNAldtN20R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 2	GSM4007806	GSM4007806: zfRNAldtN20R2; Danio rerio; RNA Seq	GSM4007806		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF6N_S9_R1_001.fastq.gz THoa-DF6N_S9_R2_001.fastq.gz	fastq fastq	7098730131.0	47579801.0	GSM4007806 r1	0:74.60 1:74.59	A:1717050162;C:1797575844;G:1860363186;T:1720884708;N:2856231	74	74	1717050162	1797575844	1860363186	1720884708	2856231	SRX6657777	SRS5218238	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93627	0.93912	0.23916	0.25175	0.80945	0.81418	0.67342	0.68259	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53541	53541	SRR9906819	SRX6657776	SRS5218237	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN20R1	GSM4007805	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 1	zfRNAldtN20R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:20hr\|replicate:Replicate 1	GSM4007805	GSM4007805: zfRNAldtN20R1; Danio rerio; RNA Seq	GSM4007805		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF5N_S8_R1_001.fastq.gz THoa-DF5N_S8_R2_001.fastq.gz	fastq fastq	7507942092.0	50334342.0	GSM4007805 r1	0:74.59 1:74.57	A:1866081920;C:1827112880;G:1922774342;T:1888960357;N:3012593	74	74	1866081920	1827112880	1922774342	1888960357	3012593	SRX6657776	SRS5218237	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.92572	0.93469	0.27326	0.28815	0.79084	0.79707	0.61558	0.63121	75	74	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53542	53542	SRR9906818	SRX6657775	SRS5218236	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN10R2	GSM4007804	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 2	zfRNAldtN10R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 2	GSM4007804	GSM4007804: zfRNAldtN10R2; Danio rerio; RNA Seq	GSM4007804		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF4N_S4_R1_001.fastq.gz THoa-DF4N_S4_R2_001.fastq.gz	fastq fastq	9118674847.0	60348350.0	GSM4007804 r1	0:75.55 1:75.55	A:2354247285;C:2165731401;G:2244032848;T:2353621167;N:1042146	75	75	2354247285	2165731401	2244032848	2353621167	1042146	SRX6657775	SRS5218236	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.90175	0.91595	0.25813	0.27158	0.79125	0.7931	0.62118	0.61894	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53543	53543	SRR9906817	SRX6657774	SRS5218235	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN10R1R2	GSM4007803	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 1	zfRNAldtN10R1R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 1	GSM4007803	GSM4007803: zfRNAldtN10R1R2; Danio rerio; RNA Seq	GSM4007803		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF2N_S4_R1_001.fastq.gz THoa-DF2N_S4_R2_001.fastq.gz	fastq fastq	6920389304.0	45528877.0	GSM4007803 r1	0:76 1:76	A:1832467265;C:1590107325;G:1661000950;T:1836680423;N:133341	76	76	1832467265	1590107325	1661000950	1836680423	133341	SRX6657774	SRS5218235	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.89667	0.91615	0.32531	0.34748	0.78407	0.78628	0.61109	0.59996	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53544	53544	SRR9906816	SRX6657773	SRS5218234	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN10R1R1	GSM4007802	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 1	zfRNAldtN10R1R1	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:10hr\|replicate:Replicate 1	GSM4007802	GSM4007802: zfRNAldtN10R1R1; Danio rerio; RNA Seq	GSM4007802		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		DF2N_S4_R1_001.fastq.gz DF2N_S4_R2_001.fastq.gz	fastq fastq	6701567912.0	44400966.0	GSM4007802 r1	0:75.49 1:75.44	A:1688384411;C:1625844846;G:1698926520;T:1686384951;N:2027184	75	75	1688384411	1625844846	1698926520	1686384951	2027184	SRX6657773	SRS5218234	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.91379	0.93036	0.29573	0.31837	0.80034	0.8017	0.638	0.65469	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53545	53545	SRR9906815	SRX6657772	SRS5218233	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN04R2	GSM4007801	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 2	zfRNAldtN04R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 2	GSM4007801	GSM4007801: zfRNAldtN04R2; Danio rerio; RNA Seq	GSM4007801		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF3N_S3_R1_001.fastq.gz THoa-DF3N_S3_R2_001.fastq.gz	fastq fastq	9452762624.0	62556061.0	GSM4007801 r1	0:75.55 1:75.56	A:2418410246;C:2278741513;G:2354276985;T:2400236180;N:1097700	75	75	2418410246	2278741513	2354276985	2400236180	1097700	SRX6657772	SRS5218233	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.90533	0.91159	0.20572	0.21726	0.81349	0.81436	0.6425	0.64845	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53546	53546	SRR9906814	SRX6657771	SRS5218232	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtN04R1R2	GSM4007800	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 1	zfRNAldtN04R1R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP \|time:4hr\|replicate:Replicate 1	GSM4007800	GSM4007800: zfRNAldtN04R1R2; Danio rerio; RNA Seq	GSM4007800		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF1N_S3_R1_001.fastq.gz THoa-DF1N_S3_R2_001.fastq.gz	fastq fastq	6443366488.0	42390569.0	GSM4007800 r1	0:76 1:76	A:1668027282;C:1512803937;G:1592154543;T:1670256264;N:124462	76	76	1668027282	1512803937	1592154543	1670256264	124462	SRX6657771	SRS5218232	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.90685	0.92348	0.30206	0.32259	0.80016	0.80156	0.63847	0.61929	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53547	53547	SRR9906813	SRX6657770	SRS5218231	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtP36R2R2	GSM4007799	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 2	zfRNAldtP36R2R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 2	GSM4007799	GSM4007799: zfRNAldtP36R2R2; Danio rerio; RNA Seq	GSM4007799		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF8P_S9_R1_001.fastq.gz THoa-DF8P_S9_R2_001.fastq.gz	fastq fastq	6236494032.0	41029566.0	GSM4007799 r1	0:76 1:76	A:1465414386;C:1634912062;G:1681819477;T:1454230315;N:117792	76	76	1465414386	1634912062	1681819477	1454230315	117792	SRX6657770	SRS5218231	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.94408	0.94952	0.15494	0.16176	0.82404	0.82544	0.67236	0.65741	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53548	53548	SRR9906812	SRX6657769	SRS5218230	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtP36R1R2	GSM4007798	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 1	zfRNAldtP36R1R2	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP+\|time:36hr\|replicate:Replicate 1	GSM4007798	GSM4007798: zfRNAldtP36R1R2; Danio rerio; RNA Seq	GSM4007798		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		THoa-DF7P_S10_R1_001.fastq.gz THoa-DF7P_S10_R2_001.fastq.gz	fastq fastq	7484077973.0	50162298.0	GSM4007798 r1	0:74.59 1:74.61	A:1782486863;C:1922264544;G:1989068688;T:1787280217;N:2977661	74	74	1782486863	1922264544	1989068688	1787280217	2977661	SRX6657769	SRS5218230	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.95471	0.95346	0.15186	0.1567	0.80332	0.80736	0.64996	0.66954	74	74	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System
53549	53549	SRR9906811	SRX6657768	SRS5218229	SRP217505	PRJNA558770	Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia	GSE135406	Other	Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.	pubmed:33004674;pubmed:35259089;pubmed:38123561	zfRNAldtP20R3	GSM4007797	source name:Retina\|tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	zfRNAldtP20R3	Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.	Retina	For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.	To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.	tissue:Retina\|genotype:Tg[gfap:EGFP]nt11 albino\|condition:Light damage\|cell population of facs sorting:GFP+\|time:20hr\|replicate:Replicate 2	GSM4007797	GSM4007797: zfRNAldtP20R3; Danio rerio; RNA Seq	GSM4007797		1	RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP217505		DF31P_S8_R1_001.fastq.gz DF31P_S8_R2_001.fastq.gz	fastq fastq	8153845075.0	54684638.0	GSM4007797 r1	0:74.54 1:74.57	A:2035354223;C:2023329236;G:2076788826;T:2016246616;N:2126174	74	74	2035354223	2023329236	2076788826	2016246616	2126174	SRX6657768	SRS5218229	SRA934563	GEO	Ophthalmology, Johns Hopkins University	2	0.93265	0.94088	0.15684	0.16053	0.80846	0.81044	0.67966	0.68311	75	72	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	trueseq	sc_generic	bulk	bulk	United States	2019-08-05	Multi-stage	Multi-stage	Eye	Sensory System

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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");;