metadata: run_metadata: 354 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation

354 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation_coarse = "Sensory System"

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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
34962	34962	SRR32588719	SRX27895232	SRS24266231	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.		Iso Seq RNA from Danio rerio	C2 F2 F EYE	strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:female\|tissue:eye\|BioSampleModel:Model organism or animal									Iso Seq RNA from eye	C2 F2 F EYE	C2 F2 F EYE	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II	SRP568323	m64467e_240703_141215.skera.flnc.fastq.gz	fastq	36628626441.0	15348616.0	m64467e 240703 141215.skera.flnc.fastq.gz	0:2386.44	A:10655476547;C:7616418469;G:7889834035;T:10466897390;N:0	2386		10655476547	7616418469	7889834035	10466897390	0	SRX27895232	SRS24266231	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute							T	long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Eye	Sensory System
34972	34972	SRR32588729	SRX27895222	SRS24266219	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.		Iso Seq RNA from Danio rerio	C2 F2 M EYE	strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:male\|tissue:eye\|BioSampleModel:Model organism or animal									Iso Seq RNA from eye	C2 F2 M EYE	C2 F2 M EYE	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II	SRP568323	m84270_240904_172441_s3.skera.flnc.fastq.gz	fastq	80921799737.0	39038804.0	m84270 240904 172441 s3.skera.flnc.fastq.gz	0:2072.86	A:23445079372;C:17292916271;G:17758249005;T:22425555089;N:0	2072		23445079372	17292916271	17758249005	22425555089	0	SRX27895222	SRS24266219	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute							T	long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Eye	Sensory System
36699	36699	SRR835180	SRX271976	SRS416272	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeh 143h 31 436	GSM1129638	tissue:retinal pigmented epithelium\|hpf	rpeh 143h 31 436	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129638	GSM1129638: rpeh 143h 31 436; Danio rerio; RNA Seq	GSM1129638 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129638	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeh_143h_31_436_ATCT.fq.bz2	fastq	233585940.0	5561570.0	GSM1129638 r1	0:42	A:55598949;C:61313735;G:51248287;T:65240290;N:184679	42		55598949	61313735	51248287	65240290	184679	SRX271976	SRS416272	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.81459	0.17202	0.85642	0.45987	42	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
36700	36700	SRR835179	SRX271975	SRS416270	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeh 143h 31 351	GSM1129637	tissue:retinal pigmented epithelium\|hpf	rpeh 143h 31 351	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129637	GSM1129637: rpeh 143h 31 351; Danio rerio; RNA Seq	GSM1129637 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129637	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeh_143h_31_351_ATCT.fq.bz2	fastq	130461444.0	3623929.0	GSM1129637 r1	0:36	A:30448136;C:34618233;G:27756164;T:37637830;N:1081	36		30448136	34618233	27756164	37637830	1081	SRX271975	SRS416270	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.80013	0.18213	0.85673	0.46503	36	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
36701	36701	SRR835178	SRX271974	SRS416271	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeh 86h 33 436	GSM1129636	tissue:retinal pigmented epithelium\|hpf	rpeh 86h 33 436	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129636	GSM1129636: rpeh 86h 33 436; Danio rerio; RNA Seq	GSM1129636 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129636	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeh_86h_33_436_CTTT.fq.bz2	fastq	375701970.0	8945285.0	GSM1129636 r1	0:42	A:79041659;C:105394908;G:87165145;T:103778792;N:321466	42		79041659	105394908	87165145	103778792	321466	SRX271974	SRS416271	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.69127	0.03078	0.88016	0.45532	42	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
36702	36702	SRR835177	SRX271973	SRS416269	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeh 86h 33 351	GSM1129635	tissue:retinal pigmented epithelium\|hpf	rpeh 86h 33 351	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129635	GSM1129635: rpeh 86h 33 351; Danio rerio; RNA Seq	GSM1129635 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129635	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeh_86h_33_351_CTTT.fq.bz2	fastq	94727196.0	2631311.0	GSM1129635 r1	0:36	A:19052917;C:27063976;G:21468497;T:27141011;N:795	36		19052917	27063976	21468497	27141011	795	SRX271973	SRS416269	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.63527	0.03789	0.88118	0.42915	36	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
36703	36703	SRR835176	SRX271972	SRS416268	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeh 86h 32 436	GSM1129634	tissue:retinal pigmented epithelium\|hpf	rpeh 86h 32 436	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129634	GSM1129634: rpeh 86h 32 436; Danio rerio; RNA Seq	GSM1129634 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129634	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeh_86h_32_436_ACGT.fq.bz2	fastq	455528976.0	10845928.0	GSM1129634 r1	0:42	A:104114782;C:122028793;G:112429635;T:116603169;N:352597	42		104114782	122028793	112429635	116603169	352597	SRX271972	SRS416268	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.80425	0.07901	0.83999	0.53561	42	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
36704	36704	SRR835175	SRX271971	SRS416267	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeh 86h 32 351	GSM1129633	tissue:retinal pigmented epithelium\|hpf	rpeh 86h 32 351	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129633	GSM1129633: rpeh 86h 32 351; Danio rerio; RNA Seq	GSM1129633 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129633	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeh_86h_32_351_ACGT.fq.bz2	fastq	124319592.0	3453322.0	GSM1129633 r1	0:36	A:28020637;C:33641464;G:30211380;T:32445126;N:985	36		28020637	33641464	30211380	32445126	985	SRX271971	SRS416267	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.80002	0.09087	0.83755	0.53605	36	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
36705	36705	SRR835174	SRX271970	SRS416266	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeleye 77h 48 440	GSM1129632	tissue:retinal pigmented epithelium\|hpf	rpeleye 77h 48 440	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129632	GSM1129632: rpeleye 77h 48 440; Danio rerio; RNA Seq	GSM1129632 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129632	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeleye_77h_48_440.fq.bz2	fastq	229484094.0	5463907.0	GSM1129632 r1	0:42	A:52877590;C:49045786;G:47421087;T:80125185;N:14446	42		52877590	49045786	47421087	80125185	14446	SRX271970	SRS416266	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.8073	0.19597	0.84017	0.51585	42	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
36706	36706	SRR835173	SRX271969	SRS416265	SRP021517	PRJNA198908	Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin	GSE46387	Transcriptome Analysis	In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing	pubmed:23874447	rpeleye 77h 47 440	GSM1129631	tissue:retinal pigmented epithelium\|hpf	rpeleye 77h 47 440	Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library	retinal pigmented epithelium		This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…		hpf	GSM1129631	GSM1129631: rpeleye 77h 47 440; Danio rerio; RNA Seq	GSM1129631 1		1	This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…	GEO Accession:GSM1129631	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP021517	rpeleye_77h_47_440.fq.bz2	fastq	227857098.0	5425169.0	GSM1129631 r1	0:42	A:56239823;C:56488585;G:57018473;T:58097500;N:12717	42		56239823	56488585	57018473	58097500	12717	SRX271969	SRS416265	SRA074390	GEO	Rob Mitra, Genetics, Washington University	1	0.71632	0.09237	0.85602	0.53769	42	B	usable mapping rate	illumina	hiseq_era	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2013-04-25	Larval	Larval	Eye	Sensory System
37994	37994	SRR1265763	SRX529157	SRS598854	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Eye Replicate 3 sRNAseq	GSM1376646	source name:Eye\|tissue:Eye\|genetic background:Wild type Singapore strain	Eye Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Eye	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Eye\|genetic background:Wild type Singapore strain	GSM1376646	GSM1376646: Eye Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376646		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376646	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZE014_GCCAAT_L005_R1.fastq.gz	fastq	299134784.0	3935984.0	GSM1376646 r1	0:76	A:62089027;C:82689882;G:78294122;T:76032871;N:28882	76		62089027	82689882	78294122	76032871	28882	SRX529157	SRS598854	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00078	8e-05	0.99892	0.66406	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Eye	Sensory System
37995	37995	SRR1265762	SRX529156	SRS598853	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Eye Replicate 2 sRNAseq	GSM1376645	source name:Eye\|tissue:Eye\|genetic background:Wild type Singapore strain	Eye Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Eye	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Eye\|genetic background:Wild type Singapore strain	GSM1376645	GSM1376645: Eye Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376645		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376645	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZE013_ACAGTG_L005_R1.fastq.gz	fastq	622465080.0	8190330.0	GSM1376645 r1	0:76	A:127621827;C:166524813;G:172833628;T:155425094;N:59718	76		127621827	166524813	172833628	155425094	59718	SRX529156	SRS598853	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00132	7e-05	0.99886	0.66956	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Eye	Sensory System
37996	37996	SRR1265761	SRX529155	SRS598852	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Eye Replicate 1 sRNAseq	GSM1376644	source name:Eye\|tissue:Eye\|genetic background:Wild type Singapore strain	Eye Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Eye	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Eye\|genetic background:Wild type Singapore strain	GSM1376644	GSM1376644: Eye Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376644		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376644	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZE008_TGACCA_L005_R1.fastq.gz	fastq	906617148.0	11929173.0	GSM1376644 r1	0:76	A:188700519;C:246755919;G:238402849;T:232669963;N:87898	76		188700519	246755919	238402849	232669963	87898	SRX529155	SRS598852	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00073	4e-05	0.9991	0.61788	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Eye	Sensory System
38046	38046	SRR1427469	SRX612649	SRS643610	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration	pubmed:25220904	28d	GSM1417152	source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	28d	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417152	GSM1417152: 28d; Danio rerio; miRNA Seq	GSM1417152		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417152	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	SRP043465	28d.fq	bam	694299184.0	32089203.0	GSM1417152 r1	0:21.64 1:0	A:174747494;C:132129648;G:193085254;T:194336788;N:0	21	0	174747494	132129648	193085254	194336788	0	SRX612649	SRS643610	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.93434	0.05272	0.98831	0.56642	23	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
38047	38047	SRR1427468	SRX612648	SRS643609	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration	pubmed:25220904	72h	GSM1417151	source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	72h	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417151	GSM1417151: 72h; Danio rerio; miRNA Seq	GSM1417151		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417151	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	SRP043465	72h.fq	fastq	689263089.0	31419317.0	GSM1417151 r1	0:21.94 1:0	A:161567060;C:125003691;G:193763870;T:208928468;N:0	21	0	161567060	125003691	193763870	208928468	0	SRX612648	SRS643609	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.93237	0.03751	0.98774	0.51765	20	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
38048	38048	SRR1427467	SRX612647	SRS643608	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration	pubmed:25220904	0h	GSM1417150	source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	0h	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417150	GSM1417150: 0h; Danio rerio; miRNA Seq	GSM1417150		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417150	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	SRP043465	0h.bam	fastq	3005859202.0	134278309.0	GSM1417150 r1	0:22.39	A:762111385;C:628084257;G:836553469;T:779110091;N:0	22		762111385	628084257	836553469	779110091	0	SRX612647	SRS643608	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.94362	0.03903	0.99093	0.5848	22	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
39680	39680	SRR2039721	SRX1038073	SRS945231	SRP058706	PRJNA284916	Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2	GSE69219	Other	The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2 resulting in red shifted spectral sensitivity of the visual system. We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone so we profiled the RPE from TH and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE conducted in triplicate	pubmed:26549260	zebrafish RPE V3	GSM1695527	source name:retinal pigment epithelium RPE\|treatment:Vehicle control\|region of rpe:N/A\|tissue:retinal pigment epithelium	zebrafish RPE V3	bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One 2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset curated zebrafish transcriptome with cyp27 family transcripts added PLoS One 2013. 87: p. e67801 included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data	retinal pigment epithelium RPE		Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	Zebrafish were treated for three weeks with TH or a vehicle control.	treatment:Vehicle control\|region of rpe:N/A\|tissue:retinal pigment epithelium	GSM1695527	GSM1695527: zebrafish RPE V3; Danio rerio; RNA Seq	GSM1695527		1	Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	GEO Accession:GSM1695527	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058706	zebrafish_RPE_V3.fq.gz	fastq	1398879800.0	27977596.0	GSM1695527 r1	0:50	A:372827112;C:318907071;G:322799013;T:383834897;N:511707	50		372827112	318907071	322799013	383834897	511707	SRX1038073	SRS945231	SRA269915	GEO	Washington University School of Medicine	1	0.86882	0.25203	0.75572	0.65651	50	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	United States	2015-05-26	Undetermined	Undetermined	Eye	Sensory System
39681	39681	SRR2039720	SRX1038072	SRS945232	SRP058706	PRJNA284916	Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2	GSE69219	Other	The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2 resulting in red shifted spectral sensitivity of the visual system. We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone so we profiled the RPE from TH and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE conducted in triplicate	pubmed:26549260	zebrafish RPE V2	GSM1695526	source name:retinal pigment epithelium RPE\|treatment:Vehicle control\|region of rpe:N/A\|tissue:retinal pigment epithelium	zebrafish RPE V2	bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One 2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset curated zebrafish transcriptome with cyp27 family transcripts added PLoS One 2013. 87: p. e67801 included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data	retinal pigment epithelium RPE		Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	Zebrafish were treated for three weeks with TH or a vehicle control.	treatment:Vehicle control\|region of rpe:N/A\|tissue:retinal pigment epithelium	GSM1695526	GSM1695526: zebrafish RPE V2; Danio rerio; RNA Seq	GSM1695526		1	Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	GEO Accession:GSM1695526	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058706	zebrafish_RPE_V2.fq.gz	fastq	1424267450.0	28485349.0	GSM1695526 r1	0:50	A:384966484;C:318922158;G:323424610;T:396433148;N:521050	50		384966484	318922158	323424610	396433148	521050	SRX1038072	SRS945232	SRA269915	GEO	Washington University School of Medicine	1	0.85592	0.26231	0.74614	0.63068	50	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	United States	2015-05-26	Undetermined	Undetermined	Eye	Sensory System
39682	39682	SRR2039719	SRX1038071	SRS945233	SRP058706	PRJNA284916	Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2	GSE69219	Other	The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2 resulting in red shifted spectral sensitivity of the visual system. We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone so we profiled the RPE from TH and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE conducted in triplicate	pubmed:26549260	zebrafish RPE V1	GSM1695525	source name:retinal pigment epithelium RPE\|treatment:Vehicle control\|region of rpe:N/A\|tissue:retinal pigment epithelium	zebrafish RPE V1	bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One 2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset curated zebrafish transcriptome with cyp27 family transcripts added PLoS One 2013. 87: p. e67801 included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data	retinal pigment epithelium RPE		Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	Zebrafish were treated for three weeks with TH or a vehicle control.	treatment:Vehicle control\|region of rpe:N/A\|tissue:retinal pigment epithelium	GSM1695525	GSM1695525: zebrafish RPE V1; Danio rerio; RNA Seq	GSM1695525		1	Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	GEO Accession:GSM1695525	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058706	zebrafish_RPE_V1.fq.gz	fastq	1562666150.0	31253323.0	GSM1695525 r1	0:50	A:425809315;C:346680173;G:352748774;T:436855950;N:571938	50		425809315	346680173	352748774	436855950	571938	SRX1038071	SRS945233	SRA269915	GEO	Washington University School of Medicine	1	0.8622	0.24448	0.74659	0.63481	50	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	United States	2015-05-26	Undetermined	Undetermined	Eye	Sensory System
39683	39683	SRR2039718	SRX1038070	SRS945234	SRP058706	PRJNA284916	Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2	GSE69219	Other	The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2 resulting in red shifted spectral sensitivity of the visual system. We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone so we profiled the RPE from TH and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE conducted in triplicate	pubmed:26549260	zebrafish RPE T3	GSM1695524	source name:retinal pigment epithelium RPE\|treatment:Thyroid horm1\|region of rpe:N/A\|tissue:retinal pigment epithelium	zebrafish RPE T3	bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One 2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset curated zebrafish transcriptome with cyp27 family transcripts added PLoS One 2013. 87: p. e67801 included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data	retinal pigment epithelium RPE		Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	Zebrafish were treated for three weeks with TH or a vehicle control.	treatment:Thyroid horm1\|region of rpe:N/A\|tissue:retinal pigment epithelium	GSM1695524	GSM1695524: zebrafish RPE T3; Danio rerio; RNA Seq	GSM1695524		1	Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	GEO Accession:GSM1695524	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058706	zebrafish_RPE_T3.fq.gz	fastq	1384311250.0	27686225.0	GSM1695524 r1	0:50	A:365623713;C:318733172;G:322931194;T:376515371;N:507800	50		365623713	318733172	322931194	376515371	507800	SRX1038070	SRS945234	SRA269915	GEO	Washington University School of Medicine	1	0.86222	0.24783	0.76124	0.64632	50	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	United States	2015-05-26	Undetermined	Undetermined	Eye	Sensory System
39684	39684	SRR2039717	SRX1038069	SRS945235	SRP058706	PRJNA284916	Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2	GSE69219	Other	The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2 resulting in red shifted spectral sensitivity of the visual system. We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone so we profiled the RPE from TH and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE conducted in triplicate	pubmed:26549260	zebrafish RPE T2	GSM1695523	source name:retinal pigment epithelium RPE\|treatment:Thyroid horm1\|region of rpe:N/A\|tissue:retinal pigment epithelium	zebrafish RPE T2	bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One 2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset curated zebrafish transcriptome with cyp27 family transcripts added PLoS One 2013. 87: p. e67801 included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data	retinal pigment epithelium RPE		Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	Zebrafish were treated for three weeks with TH or a vehicle control.	treatment:Thyroid horm1\|region of rpe:N/A\|tissue:retinal pigment epithelium	GSM1695523	GSM1695523: zebrafish RPE T2; Danio rerio; RNA Seq	GSM1695523		1	Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	GEO Accession:GSM1695523	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058706	zebrafish_RPE_T2.fq.gz	fastq	1519161100.0	30383222.0	GSM1695523 r1	0:50	A:400594372;C:350805128;G:354718825;T:412492575;N:550200	50		400594372	350805128	354718825	412492575	550200	SRX1038069	SRS945235	SRA269915	GEO	Washington University School of Medicine	1	0.86836	0.26137	0.75022	0.60251	50	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	United States	2015-05-26	Undetermined	Undetermined	Eye	Sensory System
39685	39685	SRR2039716	SRX1038068	SRS945236	SRP058706	PRJNA284916	Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2	GSE69219	Other	The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2 resulting in red shifted spectral sensitivity of the visual system. We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone so we profiled the RPE from TH and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE conducted in triplicate	pubmed:26549260	zebrafish RPE T1	GSM1695522	source name:retinal pigment epithelium RPE\|treatment:Thyroid horm1\|region of rpe:N/A\|tissue:retinal pigment epithelium	zebrafish RPE T1	bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One 2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset curated zebrafish transcriptome with cyp27 family transcripts added PLoS One 2013. 87: p. e67801 included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data	retinal pigment epithelium RPE		Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	Zebrafish were treated for three weeks with TH or a vehicle control.	treatment:Thyroid horm1\|region of rpe:N/A\|tissue:retinal pigment epithelium	GSM1695522	GSM1695522: zebrafish RPE T1; Danio rerio; RNA Seq	GSM1695522		1	Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.	GEO Accession:GSM1695522	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058706	zebrafish_RPE_T1.fq.gz	fastq	805113700.0	16102274.0	GSM1695522 r1	0:50	A:218678280;C:181598232;G:182588099;T:221957441;N:291648	50		218678280	181598232	182588099	221957441	291648	SRX1038068	SRS945236	SRA269915	GEO	Washington University School of Medicine	1	0.86363	0.25795	0.7334	0.5942	50	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	United States	2015-05-26	Undetermined	Undetermined	Eye	Sensory System
39795	39795	SRR2145848	SRX1133838	SRS1023794	SRP062048	PRJNA291981	Yap and Taz regulate retinal pigment epithelial cell fate	GSE71681	Transcriptome Analysis	The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.	pubmed:26209646	YapS87A rep3	GSM1844492	source name:whole eye\|developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A	YapS87A rep3	RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample.	whole eye		Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.		developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A	GSM1844492	GSM1844492: YapS87A rep3; Danio rerio; RNA Seq	GSM1844492		1	Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.	GEO Accession:GSM1844492	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP062048	YapS87A_3_sequence.txt.gz	fastq	1680502581.0	32951031.0	GSM1844492 r1	0:51	A:431882743;C:376993099;G:378520286;T:464147117;N:28959336	51		431882743	376993099	378520286	464147117	28959336	SRX1133838	SRS1023794	SRA282186	GEO	Medical College of Wisconsin	1	0.9063	0.08492	0.73279	0.45445	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2015-08-05	Pharyngula	Embryo	Eye	Sensory System
39796	39796	SRR2145847	SRX1133837	SRS1023795	SRP062048	PRJNA291981	Yap and Taz regulate retinal pigment epithelial cell fate	GSE71681	Transcriptome Analysis	The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.	pubmed:26209646	YapS87A rep2	GSM1844491	source name:whole eye\|developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A	YapS87A rep2	RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample.	whole eye		Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.		developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A	GSM1844491	GSM1844491: YapS87A rep2; Danio rerio; RNA Seq	GSM1844491		1	Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.	GEO Accession:GSM1844491	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP062048	YapS87A_2_sequence.txt.gz	fastq	1742004705.0	34156955.0	GSM1844491 r1	0:51	A:447373634;C:393295480;G:396777263;T:483090843;N:21467485	51		447373634	393295480	396777263	483090843	21467485	SRX1133837	SRS1023795	SRA282186	GEO	Medical College of Wisconsin	1	0.90563	0.0858	0.72707	0.46494	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2015-08-05	Pharyngula	Embryo	Eye	Sensory System
39797	39797	SRR2145846	SRX1133836	SRS1023796	SRP062048	PRJNA291981	Yap and Taz regulate retinal pigment epithelial cell fate	GSE71681	Transcriptome Analysis	The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.	pubmed:26209646	YapS87A rep1	GSM1844490	source name:whole eye\|developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A	YapS87A rep1	RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample.	whole eye		Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.		developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A	GSM1844490	GSM1844490: YapS87A rep1; Danio rerio; RNA Seq	GSM1844490		1	Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.	GEO Accession:GSM1844490	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP062048	YapS87A_1_sequence.txt.gz	fastq	1605602451.0	31482401.0	GSM1844490 r1	0:51	A:416296166;C:357147049;G:359581538;T:444847570;N:27730128	51		416296166	357147049	359581538	444847570	27730128	SRX1133836	SRS1023796	SRA282186	GEO	Medical College of Wisconsin	1	0.90209	0.08942	0.72979	0.47171	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2015-08-05	Pharyngula	Embryo	Eye	Sensory System
39798	39798	SRR2145845	SRX1133835	SRS1023797	SRP062048	PRJNA291981	Yap and Taz regulate retinal pigment epithelial cell fate	GSE71681	Transcriptome Analysis	The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.	pubmed:26209646	WT rep3	GSM1844489	source name:whole eye\|developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4 sibling control	WT rep3	RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample.	whole eye		Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.		developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4 sibling control	GSM1844489	GSM1844489: WT rep3; Danio rerio; RNA Seq	GSM1844489		1	Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.	GEO Accession:GSM1844489	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP062048	WT_3_sequence.txt.gz	fastq	1609588305.0	31560555.0	GSM1844489 r1	0:51	A:412663150;C:358619332;G:364439350;T:446055681;N:27810792	51		412663150	358619332	364439350	446055681	27810792	SRX1133835	SRS1023797	SRA282186	GEO	Medical College of Wisconsin	1	0.92186	0.07797	0.73499	0.47006	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2015-08-05	Pharyngula	Embryo	Eye	Sensory System
39799	39799	SRR2145844	SRX1133834	SRS1023798	SRP062048	PRJNA291981	Yap and Taz regulate retinal pigment epithelial cell fate	GSE71681	Transcriptome Analysis	The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.	pubmed:26209646	WT rep2	GSM1844488	source name:whole eye\|developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4 sibling control	WT rep2	RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample.	whole eye		Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.		developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4 sibling control	GSM1844488	GSM1844488: WT rep2; Danio rerio; RNA Seq	GSM1844488		1	Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.	GEO Accession:GSM1844488	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP062048	WT_2_sequence.txt.gz	fastq	1637145594.0	32100894.0	GSM1844488 r1	0:51	A:414176151;C:369403072;G:372539483;T:452762354;N:28264534	51		414176151	369403072	372539483	452762354	28264534	SRX1133834	SRS1023798	SRA282186	GEO	Medical College of Wisconsin	1	0.92352	0.08166	0.7318	0.47492	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2015-08-05	Pharyngula	Embryo	Eye	Sensory System
39800	39800	SRR2145843	SRX1133833	SRS1023799	SRP062048	PRJNA291981	Yap and Taz regulate retinal pigment epithelial cell fate	GSE71681	Transcriptome Analysis	The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.	pubmed:26209646	WT rep1	GSM1844487	source name:whole eye\|developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4 sibling control	WT rep1	RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample.	whole eye		Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.		developmental stage:36 hpf\|tissue:whole eye\|genotype:vsx2:Gal4 sibling control	GSM1844487	GSM1844487: WT rep1; Danio rerio; RNA Seq	GSM1844487		1	Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.	GEO Accession:GSM1844487	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP062048	WT_1_sequence.txt.gz	fastq	1666445961.0	32675411.0	GSM1844487 r1	0:51	A:421437796;C:380026405;G:379400332;T:465027467;N:20553961	51		421437796	380026405	379400332	465027467	20553961	SRX1133833	SRS1023799	SRA282186	GEO	Medical College of Wisconsin	1	0.91935	0.0764	0.73083	0.47263	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2015-08-05	Pharyngula	Embryo	Eye	Sensory System
41319	41319	SRR4241545	SRX2162516	SRS1690572	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	16 hpl Replicate 3	GSM2309786	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 16 hours post lesion	16 hpl Replicate 3	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia	Free swimming fish exposed to intense light >120 000 lux for 30 minutes. Retinas harvested at 16 hours post lesion hpl.	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 16 hours post lesion	GSM2309786	GSM2309786: 16 hpl Replicate 3; Danio rerio; RNA Seq	GSM2309786		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309786	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	16hpl3.fq.gz	fastq	2321192665.0	27308149.0	GSM2309786 r1	0:85	A:578506517;C:590753476;G:555712960;T:595943815;N:275897	85		578506517	590753476	555712960	595943815	275897	SRX2162516	SRS1690572	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.56954	0.07699	0.7667	0.49583	85	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41320	41320	SRR4241544	SRX2162515	SRS1690571	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	16 hpl Replicate 2	GSM2309785	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 16 hours post lesion	16 hpl Replicate 2	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia	Free swimming fish exposed to intense light >120 000 lux for 30 minutes. Retinas harvested at 16 hours post lesion hpl.	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 16 hours post lesion	GSM2309785	GSM2309785: 16 hpl Replicate 2; Danio rerio; RNA Seq	GSM2309785		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309785	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	16hpl2.fq.gz	fastq	3238182160.0	42607660.0	GSM2309785 r1	0:76	A:810206011;C:813290062;G:763305237;T:851164602;N:216248	76		810206011	813290062	763305237	851164602	216248	SRX2162515	SRS1690571	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.62326	0.07359	0.75988	0.51307	76	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41321	41321	SRR4241543	SRX2162514	SRS1690570	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	16 hpl Replicate 1	GSM2309784	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 16 hours post lesion	16 hpl Replicate 1	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia	Free swimming fish exposed to intense light >120 000 lux for 30 minutes. Retinas harvested at 16 hours post lesion hpl.	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 16 hours post lesion	GSM2309784	GSM2309784: 16 hpl Replicate 1; Danio rerio; RNA Seq	GSM2309784		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309784	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	16hpl1.fq.gz	fastq	3435972692.0	45210167.0	GSM2309784 r1	0:76	A:880014076;C:841772051;G:804598316;T:909404579;N:183670	76		880014076	841772051	804598316	909404579	183670	SRX2162514	SRS1690570	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.64656	0.09009	0.75891	0.5128	76	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41322	41322	SRR4241542	SRX2162513	SRS1690569	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	8 hpl Replicate 3	GSM2309783	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 8 hours post lesion	8 hpl Replicate 3	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia	Free swimming fish exposed to intense light >120 000 lux for 30 minutes. Retinas harvested at 8 hours post lesion hpl.	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 8 hours post lesion	GSM2309783	GSM2309783: 8 hpl Replicate 3; Danio rerio; RNA Seq	GSM2309783		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309783	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	8hpl3.fq.gz	fastq	3597377480.0	42322088.0	GSM2309783 r1	0:85	A:916908079;C:887212878;G:845446820;T:947571866;N:237837	85		916908079	887212878	845446820	947571866	237837	SRX2162513	SRS1690569	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.68294	0.09221	0.75513	0.51173	85	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41323	41323	SRR4241541	SRX2162512	SRS1690568	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	8 hpl Replicate 2	GSM2309782	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 8 hours post lesion	8 hpl Replicate 2	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia	Free swimming fish exposed to intense light >120 000 lux for 30 minutes. Retinas harvested at 8 hours post lesion hpl.	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 8 hours post lesion	GSM2309782	GSM2309782: 8 hpl Replicate 2; Danio rerio; RNA Seq	GSM2309782		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309782	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	8hpl2.fq.gz	fastq	3383830535.0	39809771.0	GSM2309782 r1	0:85	A:877804842;C:816574206;G:797587769;T:891646157;N:217561	85		877804842	816574206	797587769	891646157	217561	SRX2162512	SRS1690568	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.8038	0.11779	0.74428	0.49442	85	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41324	41324	SRR4241540	SRX2162511	SRS1690567	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	8 hpl Replicate 1	GSM2309781	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 8 hours post lesion	8 hpl Replicate 1	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia	Free swimming fish exposed to intense light >120 000 lux for 30 minutes. Retinas harvested at 8 hours post lesion hpl.	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Light lesion 8 hours post lesion	GSM2309781	GSM2309781: 8 hpl Replicate 1; Danio rerio; RNA Seq	GSM2309781		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309781	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	8hpl1.fq.gz	fastq	3381594692.0	44494667.0	GSM2309781 r1	0:76	A:868169135;C:824624603;G:801838332;T:886809873;N:152749	76		868169135	824624603	801838332	886809873	152749	SRX2162511	SRS1690567	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.77722	0.11441	0.74763	0.49325	76	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41325	41325	SRR4241539	SRX2162510	SRS1690566	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	0 hpl Replicate 3	GSM2309780	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Control unlesi1d	0 hpl Replicate 3	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia		Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Control unlesi1d	GSM2309780	GSM2309780: 0 hpl Replicate 3; Danio rerio; RNA Seq	GSM2309780		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309780	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	0hpl3.fq.gz	fastq	3973187555.0	46743383.0	GSM2309780 r1	0:85 1:0	A:997009150;C:996881236;G:947020068;T:1031688909;N:588192	85	0	997009150	996881236	947020068	1031688909	588192	SRX2162510	SRS1690566	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.58945	0.07407	0.78279	0.50593	85	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41326	41326	SRR4241538	SRX2162509	SRS1690565	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	0 hpl Replicate 2	GSM2309779	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Control unlesi1d	0 hpl Replicate 2	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia		Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Control unlesi1d	GSM2309779	GSM2309779: 0 hpl Replicate 2; Danio rerio; RNA Seq	GSM2309779		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309779	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	0hpl2.fq.gz	fastq	4118911810.0	48457786.0	GSM2309779 r1	0:85	A:1021450530;C:1050671687;G:958566189;T:1087989641;N:233763	85		1021450530	1050671687	958566189	1087989641	233763	SRX2162509	SRS1690565	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.56987	0.0771	0.77185	0.4875	85	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
41327	41327	SRR4241537	SRX2162508	SRS1690564	SRP089817	PRJNA342843	Rapid dynamic activation of Müller glial stem cell responses in zebrafish	GSE86872	Transcriptome Analysis	Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by…	pubmed:27699411	0 hpl Replicate 1	GSM2309778	source name:Müller glia\|line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Control unlesi1d	0 hpl Replicate 1	Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez or…	Müller glia		Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.		line:Tggfap:EGFPmi2002\|tissue:neural retina\|cell type:Muller glia\|age:8 month 11 month\|treatment:Control unlesi1d	GSM2309778	GSM2309778: 0 hpl Replicate 1; Danio rerio; RNA Seq	GSM2309778		1	Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter.	GEO Accession:GSM2309778	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP089817	0hpl1.fq.gz	fastq	3325321860.0	43754235.0	GSM2309778 r1	0:76	A:815858166;C:857051302;G:779310068;T:872607432;N:494892	76		815858166	857051302	779310068	872607432	494892	SRX2162508	SRS1690564	SRA470722	GEO	Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan	1	0.54029	0.08354	0.7792	0.51404	76	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-09-13	Adult	Adult	Eye	Sensory System
42018	42018	SRR5382066	SRX2677147	SRS2075568	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO shh 13	GSM2552024	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO shh 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552024	GSM2552024: NO shh 13; Danio rerio; RNA Seq	GSM2552024		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552024	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABIRAAPEI-214_1.fq.gz	fastq	843818269.0	17220781.0	GSM2552024 r1	0:49 1:0	A:221838981;C:201486730;G:194808523;T:225676801;N:7234	49	0	221838981	201486730	194808523	225676801	7234	SRX2677147	SRS2075568	SRA549807	GEO	Medical College of Wisconsin	1	0.90043	0.1077	0.68897	0.40147	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42019	42019	SRR5382067	SRX2677147	SRS2075568	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO shh 13	GSM2552024	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO shh 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552024	GSM2552024: NO shh 13; Danio rerio; RNA Seq	GSM2552024		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552024	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABIRAAPEI-214_1.fq.gz	fastq	829961510.0	16937990.0	GSM2552024 r2	0:49 1:0	A:218002306;C:198331442;G:191775017;T:221844452;N:8293	49	0	218002306	198331442	191775017	221844452	8293	SRX2677147	SRS2075568	SRA549807	GEO	Medical College of Wisconsin	1	0.90751	0.10841	0.6882	0.40509	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42020	42020	SRR5382064	SRX2677146	SRS2075567	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO shh 12	GSM2552023	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO shh 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552023	GSM2552023: NO shh 12; Danio rerio; RNA Seq	GSM2552023		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552023	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABGRAAPEI-212_1.fq.gz	fastq	840785561.0	17158889.0	GSM2552023 r1	0:49 1:0	A:221201132;C:200524999;G:193274512;T:225777636;N:7282	49	0	221201132	200524999	193274512	225777636	7282	SRX2677146	SRS2075567	SRA549807	GEO	Medical College of Wisconsin	1	0.90205	0.11292	0.68759	0.44522	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42021	42021	SRR5382065	SRX2677146	SRS2075567	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO shh 12	GSM2552023	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO shh 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552023	GSM2552023: NO shh 12; Danio rerio; RNA Seq	GSM2552023		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552023	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABGRAAPEI-212_1.fq.gz	fastq	834811089.0	17036961.0	GSM2552023 r2	0:49 1:0	A:219382137;C:199232543;G:192142641;T:224045481;N:8287	49	0	219382137	199232543	192142641	224045481	8287	SRX2677146	SRS2075567	SRA549807	GEO	Medical College of Wisconsin	1	0.90899	0.11358	0.68809	0.43149	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42022	42022	SRR5382062	SRX2677145	SRS2075566	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO shh 11	GSM2552022	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO shh 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552022	GSM2552022: NO shh 11; Danio rerio; RNA Seq	GSM2552022		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552022	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABERAAPEI-210_1.fq.gz	fastq	904157212.0	18452188.0	GSM2552022 r1	0:49 1:0	A:236992487;C:215051901;G:210839328;T:241266600;N:6896	49	0	236992487	215051901	210839328	241266600	6896	SRX2677145	SRS2075566	SRA549807	GEO	Medical College of Wisconsin	1	0.89893	0.10891	0.68465	0.44598	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42023	42023	SRR5382063	SRX2677145	SRS2075566	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO shh 11	GSM2552022	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO shh 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552022	GSM2552022: NO shh 11; Danio rerio; RNA Seq	GSM2552022		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552022	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABERAAPEI-210_1.fq.gz	fastq	896869197.0	18303453.0	GSM2552022 r2	0:49 1:0	A:234904626;C:213413392;G:209296940;T:239246543;N:7696	49	0	234904626	213413392	209296940	239246543	7696	SRX2677145	SRS2075566	SRA549807	GEO	Medical College of Wisconsin	1	0.9066	0.1098	0.68444	0.45516	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42024	42024	SRR5382060	SRX2677144	SRS2075565	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		shh 13	GSM2552021	tissue:whole larval eyes\|genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	shh 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	GSM2552021	GSM2552021: shh 13; Danio rerio; RNA Seq	GSM2552021		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552021	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABHRAAPEI-213_1.fq.gz	fastq	780154725.0	15921525.0	GSM2552021 r1	0:49 1:0	A:204493928;C:186497801;G:181452727;T:207703532;N:6737	49	0	204493928	186497801	181452727	207703532	6737	SRX2677144	SRS2075565	SRA549807	GEO	Medical College of Wisconsin	1	0.91024	0.07095	0.72874	0.42618	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42025	42025	SRR5382061	SRX2677144	SRS2075565	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		shh 13	GSM2552021	tissue:whole larval eyes\|genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	shh 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	GSM2552021	GSM2552021: shh 13; Danio rerio; RNA Seq	GSM2552021		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552021	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABHRAAPEI-213_1.fq.gz	fastq	723588096.0	14767104.0	GSM2552021 r2	0:49 1:0	A:189438629;C:173078510;G:168506893;T:192556891;N:7173	49	0	189438629	173078510	168506893	192556891	7173	SRX2677144	SRS2075565	SRA549807	GEO	Medical College of Wisconsin	1	0.91641	0.07158	0.7292	0.41626	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42026	42026	SRR5382058	SRX2677143	SRS2075564	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		shh 12	GSM2552020	tissue:whole larval eyes\|genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	shh 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	GSM2552020	GSM2552020: shh 12; Danio rerio; RNA Seq	GSM2552020		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552020	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABFRAAPEI-211_1.fq.gz	fastq	767433100.0	15661900.0	GSM2552020 r1	0:49 1:0	A:201134121;C:184183797;G:177805845;T:204302839;N:6498	49	0	201134121	184183797	177805845	204302839	6498	SRX2677143	SRS2075564	SRA549807	GEO	Medical College of Wisconsin	1	0.90254	0.10915	0.69029	0.43993	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42027	42027	SRR5382059	SRX2677143	SRS2075564	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		shh 12	GSM2552020	tissue:whole larval eyes\|genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	shh 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	GSM2552020	GSM2552020: shh 12; Danio rerio; RNA Seq	GSM2552020		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552020	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABFRAAPEI-211_1.fq.gz	fastq	748240290.0	15270210.0	GSM2552020 r2	0:49 1:0	A:195869449;C:179706491;G:173543679;T:199113253;N:7418	49	0	195869449	179706491	173543679	199113253	7418	SRX2677143	SRS2075564	SRA549807	GEO	Medical College of Wisconsin	1	0.90915	0.11014	0.68929	0.42638	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42028	42028	SRR5382056	SRX2677142	SRS2075563	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		shh 11	GSM2552019	tissue:whole larval eyes\|genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	shh 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	GSM2552019	GSM2552019: shh 11; Danio rerio; RNA Seq	GSM2552019		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552019	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABDRAAPEI-209_1.fq.gz	fastq	735291942.0	15005958.0	GSM2552019 r1	0:49 1:0	A:191931154;C:176849705;G:171335621;T:195169335;N:6127	49	0	191931154	176849705	171335621	195169335	6127	SRX2677142	SRS2075563	SRA549807	GEO	Medical College of Wisconsin	1	0.89997	0.10193	0.68771	0.42739	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42029	42029	SRR5382057	SRX2677142	SRS2075563	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		shh 11	GSM2552019	tissue:whole larval eyes\|genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	shh 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:shha eGFP\|age:5 dpf	GSM2552019	GSM2552019: shh 11; Danio rerio; RNA Seq	GSM2552019		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552019	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABDRAAPEI-209_1.fq.gz	fastq	738096016.0	15063184.0	GSM2552019 r2	0:49 1:0	A:192422803;C:177645752;G:172165273;T:195854853;N:7335	49	0	192422803	177645752	172165273	195854853	7335	SRX2677142	SRS2075563	SRA549807	GEO	Medical College of Wisconsin	1	0.90699	0.1029	0.68609	0.4169	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42030	42030	SRR5382054	SRX2677141	SRS2075562	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO bmp4 13	GSM2552018	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO bmp4 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552018	GSM2552018: NO bmp4 13; Danio rerio; RNA Seq	GSM2552018		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552018	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABCRAAPEI-208_1.fq.gz	fastq	821111277.0	16757373.0	GSM2552018 r1	0:49 1:0	A:214147667;C:197777522;G:191357044;T:217822321;N:6723	49	0	214147667	197777522	191357044	217822321	6723	SRX2677141	SRS2075562	SRA549807	GEO	Medical College of Wisconsin	1	0.90103	0.09455	0.69098	0.43034	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42031	42031	SRR5382055	SRX2677141	SRS2075562	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO bmp4 13	GSM2552018	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO bmp4 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552018	GSM2552018: NO bmp4 13; Danio rerio; RNA Seq	GSM2552018		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552018	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABCRAAPEI-208_1.fq.gz	fastq	858019596.0	17510604.0	GSM2552018 r2	0:49 1:0	A:223513905;C:206829946;G:200141599;T:227525603;N:8543	49	0	223513905	206829946	200141599	227525603	8543	SRX2677141	SRS2075562	SRA549807	GEO	Medical College of Wisconsin	1	0.90579	0.09535	0.68968	0.43592	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42032	42032	SRR5382052	SRX2677140	SRS2075561	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO bmp4 12	GSM2552017	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO bmp4 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552017	GSM2552017: NO bmp4 12; Danio rerio; RNA Seq	GSM2552017		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552017	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABARAAPEI-206_1.fq.gz	fastq	893675524.0	18238276.0	GSM2552017 r1	0:49 1:0	A:233295131;C:215015502;G:208033601;T:237323630;N:7660	49	0	233295131	215015502	208033601	237323630	7660	SRX2677140	SRS2075561	SRA549807	GEO	Medical College of Wisconsin	1	0.89549	0.10462	0.68716	0.44466	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42033	42033	SRR5382053	SRX2677140	SRS2075561	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO bmp4 12	GSM2552017	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO bmp4 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552017	GSM2552017: NO bmp4 12; Danio rerio; RNA Seq	GSM2552017		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552017	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABARAAPEI-206_1.fq.gz	fastq	897380218.0	18313882.0	GSM2552017 r2	0:49 1:0	A:234059121;C:216066812;G:208996578;T:238249498;N:8209	49	0	234059121	216066812	208996578	238249498	8209	SRX2677140	SRS2075561	SRA549807	GEO	Medical College of Wisconsin	1	0.90226	0.10464	0.68708	0.43834	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42034	42034	SRR5382050	SRX2677139	SRS2075560	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO bmp4 11	GSM2552016	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO bmp4 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552016	GSM2552016: NO bmp4 11; Danio rerio; RNA Seq	GSM2552016		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552016	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAYRAAPEI-203_1.fq.gz	fastq	761586714.0	15542586.0	GSM2552016 r1	0:49 1:0	A:199500708;C:182759688;G:176315916;T:203003924;N:6478	49	0	199500708	182759688	176315916	203003924	6478	SRX2677139	SRS2075560	SRA549807	GEO	Medical College of Wisconsin	1	0.89716	0.10544	0.6871	0.43385	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42035	42035	SRR5382051	SRX2677139	SRS2075560	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		NO bmp4 11	GSM2552016	tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO bmp4 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552016	GSM2552016: NO bmp4 11; Danio rerio; RNA Seq	GSM2552016		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552016	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAYRAAPEI-203_1.fq.gz	fastq	777977998.0	15877102.0	GSM2552016 r2	0:49 1:0	A:203591828;C:186858026;G:180247771;T:207272648;N:7725	49	0	203591828	186858026	180247771	207272648	7725	SRX2677139	SRS2075560	SRA549807	GEO	Medical College of Wisconsin	1	0.90386	0.10814	0.68728	0.44655	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42036	42036	SRR5382048	SRX2677138	SRS2075559	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		bmp4 13	GSM2552015	tissue:whole larval eyes\|genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	bmp4 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	GSM2552015	GSM2552015: bmp4 13; Danio rerio; RNA Seq	GSM2552015		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552015	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRABBRAAPEI-207_1.fq.gz	fastq	771609076.0	15747124.0	GSM2552015 r1	0:49 1:0	A:201323965;C:185589440;G:180186502;T:204502871;N:6298	49	0	201323965	185589440	180186502	204502871	6298	SRX2677138	SRS2075559	SRA549807	GEO	Medical College of Wisconsin	1	0.89654	0.09972	0.68921	0.43468	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42037	42037	SRR5382049	SRX2677138	SRS2075559	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		bmp4 13	GSM2552015	tissue:whole larval eyes\|genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	bmp4 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	GSM2552015	GSM2552015: bmp4 13; Danio rerio; RNA Seq	GSM2552015		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552015	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABBRAAPEI-207_1.fq.gz	fastq	770419650.0	15722850.0	GSM2552015 r2	0:49 1:0	A:200771257;C:185509037;G:180033647;T:204098225;N:7484	49	0	200771257	185509037	180033647	204098225	7484	SRX2677138	SRS2075559	SRA549807	GEO	Medical College of Wisconsin	1	0.90312	0.09896	0.68885	0.44175	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42038	42038	SRR5382046	SRX2677137	SRS2075558	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		bmp4 12	GSM2552014	tissue:whole larval eyes\|genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	bmp4 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	GSM2552014	GSM2552014: bmp4 12; Danio rerio; RNA Seq	GSM2552014		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552014	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAZRAAPEI-205_1.fq.gz	fastq	796994555.0	16265195.0	GSM2552014 r1	0:49 1:0	A:207611526;C:191999436;G:186148101;T:211228819;N:6673	49	0	207611526	191999436	186148101	211228819	6673	SRX2677137	SRS2075558	SRA549807	GEO	Medical College of Wisconsin	1	0.89582	0.10175	0.68816	0.43823	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42039	42039	SRR5382047	SRX2677137	SRS2075558	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		bmp4 12	GSM2552014	tissue:whole larval eyes\|genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	bmp4 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	GSM2552014	GSM2552014: bmp4 12; Danio rerio; RNA Seq	GSM2552014		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552014	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAZRAAPEI-205_1.fq.gz	fastq	814617013.0	16624837.0	GSM2552014 r2	0:49 1:0	A:211930527;C:196384410;G:190449227;T:215844442;N:8407	49	0	211930527	196384410	190449227	215844442	8407	SRX2677137	SRS2075558	SRA549807	GEO	Medical College of Wisconsin	1	0.9046	0.1045	0.68765	0.44189	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42040	42040	SRR5382044	SRX2677136	SRS2075557	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		bmp4 11	GSM2552013	tissue:whole larval eyes\|genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	bmp4 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	GSM2552013	GSM2552013: bmp4 11; Danio rerio; RNA Seq	GSM2552013		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552013	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAXRAAPEI-202_1.fq.gz	fastq	818072248.0	16695352.0	GSM2552013 r1	0:49 1:0	A:213364768;C:196897651;G:191539621;T:216263952;N:6256	49	0	213364768	196897651	191539621	216263952	6256	SRX2677136	SRS2075557	SRA549807	GEO	Medical College of Wisconsin	1	0.89563	0.10696	0.68828	0.44425	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42041	42041	SRR5382045	SRX2677136	SRS2075557	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		bmp4 11	GSM2552013	tissue:whole larval eyes\|genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	bmp4 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:Transgenic hsp70l:eGFP bmp4\|age:5 dpf	GSM2552013	GSM2552013: bmp4 11; Danio rerio; RNA Seq	GSM2552013		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552013	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAXRAAPEI-202_1.fq.gz	fastq	901802321.0	18404129.0	GSM2552013 r2	0:49 1:0	A:235005510;C:217168207;G:211265005;T:238355281;N:8318	49	0	235005510	217168207	211265005	238355281	8318	SRX2677136	SRS2075557	SRA549807	GEO	Medical College of Wisconsin	1	0.90303	0.10616	0.68665	0.4459	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Larval	Larval	Eye	Sensory System
42042	42042	SRR5382042	SRX2677135	SRS2075556	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf sclera 13	GSM2552012	tissue:choroid/sclera\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf sclera 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552012	GSM2552012: lrp2 mpf 1 mpf sclera 13; Danio rerio; RNA Seq	GSM2552012		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552012	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAATRAAPEI-223_1.fq.gz	fastq	868203658.0	17718442.0	GSM2552012 r1	0:49 1:0	A:230139963;C:203530468;G:202078408;T:232447490;N:7329	49	0	230139963	203530468	202078408	232447490	7329	SRX2677135	SRS2075556	SRA549807	GEO	Medical College of Wisconsin	1	0.89611	0.10145	0.69449	0.46437	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42043	42043	SRR5382043	SRX2677135	SRS2075556	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf sclera 13	GSM2552012	tissue:choroid/sclera\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf sclera 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552012	GSM2552012: lrp2 mpf 1 mpf sclera 13; Danio rerio; RNA Seq	GSM2552012		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552012	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAATRAAPEI-223_1.fq.gz	fastq	857269994.0	17495306.0	GSM2552012 r2	0:49 1:0	A:226970264;C:201146668;G:199712081;T:229432482;N:8499	49	0	226970264	201146668	199712081	229432482	8499	SRX2677135	SRS2075556	SRA549807	GEO	Medical College of Wisconsin	1	0.90314	0.10194	0.69443	0.47706	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42044	42044	SRR5382040	SRX2677134	SRS2075555	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf sclera 12	GSM2552011	tissue:choroid/sclera\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf sclera 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552011	GSM2552011: lrp2 mpf 1 mpf sclera 12; Danio rerio; RNA Seq	GSM2552011		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552011	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAASRAAPEI-222_1.fq.gz	fastq	818515502.0	16704398.0	GSM2552011 r1	0:49 1:0	A:214855166;C:193982000;G:192092006;T:217579339;N:6991	49	0	214855166	193982000	192092006	217579339	6991	SRX2677134	SRS2075555	SRA549807	GEO	Medical College of Wisconsin	1	0.89862	0.09572	0.69708	0.47023	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42045	42045	SRR5382041	SRX2677134	SRS2075555	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf sclera 12	GSM2552011	tissue:choroid/sclera\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf sclera 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552011	GSM2552011: lrp2 mpf 1 mpf sclera 12; Danio rerio; RNA Seq	GSM2552011		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552011	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAASRAAPEI-222_1.fq.gz	fastq	810081377.0	16532273.0	GSM2552011 r2	0:49 1:0	A:212403857;C:192140662;G:190291379;T:215237408;N:8071	49	0	212403857	192140662	190291379	215237408	8071	SRX2677134	SRS2075555	SRA549807	GEO	Medical College of Wisconsin	1	0.9065	0.09612	0.69832	0.4763	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42046	42046	SRR5382038	SRX2677133	SRS2075554	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf sclera 11	GSM2552010	tissue:choroid/sclera\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf sclera 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552010	GSM2552010: lrp2 mpf 1 mpf sclera 11; Danio rerio; RNA Seq	GSM2552010		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552010	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAARRAAPEI-221_1.fq.gz	fastq	598444497.0	12213153.0	GSM2552010 r1	0:49 1:0	A:157564573;C:141303576;G:139633698;T:159937613;N:5037	49	0	157564573	141303576	139633698	159937613	5037	SRX2677133	SRS2075554	SRA549807	GEO	Medical College of Wisconsin	1	0.89676	0.09842	0.68653	0.46649	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42047	42047	SRR5382039	SRX2677133	SRS2075554	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf sclera 11	GSM2552010	tissue:choroid/sclera\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf sclera 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552010	GSM2552010: lrp2 mpf 1 mpf sclera 11; Danio rerio; RNA Seq	GSM2552010		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552010	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAARRAAPEI-221_1.fq.gz	fastq	594578250.0	12134250.0	GSM2552010 r2	0:49 1:0	A:156350324;C:140490193;G:138869200;T:158862787;N:5746	49	0	156350324	140490193	138869200	158862787	5746	SRX2677133	SRS2075554	SRA549807	GEO	Medical College of Wisconsin	1	0.90485	0.09982	0.68521	0.4691	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42048	42048	SRR5382036	SRX2677132	SRS2075553	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf retina 13	GSM2552009	tissue:retina\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf retina 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552009	GSM2552009: lrp2 mpf 1 mpf retina 13; Danio rerio; RNA Seq	GSM2552009		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552009	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAWRAAPEI-201_1.fq.gz	fastq	754821823.0	15404527.0	GSM2552009 r1	0:49 1:0	A:206101700;C:172880224;G:168016286;T:207817318;N:6295	49	0	206101700	172880224	168016286	207817318	6295	SRX2677132	SRS2075553	SRA549807	GEO	Medical College of Wisconsin	1	0.88663	0.1569	0.70934	0.50146	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42049	42049	SRR5382037	SRX2677132	SRS2075553	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf retina 13	GSM2552009	tissue:retina\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf retina 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552009	GSM2552009: lrp2 mpf 1 mpf retina 13; Danio rerio; RNA Seq	GSM2552009		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552009	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAWRAAPEI-201_1.fq.gz	fastq	738593856.0	15073344.0	GSM2552009 r2	0:49 1:0	A:201412233;C:169280089;G:164643585;T:203250732;N:7217	49	0	201412233	169280089	164643585	203250732	7217	SRX2677132	SRS2075553	SRA549807	GEO	Medical College of Wisconsin	1	0.89286	0.15576	0.70707	0.50361	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42050	42050	SRR5382034	SRX2677131	SRS2075552	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf retina 12	GSM2552008	tissue:retina\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf retina 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552008	GSM2552008: lrp2 mpf 1 mpf retina 12; Danio rerio; RNA Seq	GSM2552008		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552008	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAVRAAPEI-227_1.fq.gz	fastq	905999220.0	18489780.0	GSM2552008 r1	0:49 1:0	A:247171602;C:207706839;G:201939609;T:249173819;N:7351	49	0	247171602	207706839	201939609	249173819	7351	SRX2677131	SRS2075552	SRA549807	GEO	Medical College of Wisconsin	1	0.88857	0.16101	0.70634	0.49492	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42051	42051	SRR5382035	SRX2677131	SRS2075552	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf retina 12	GSM2552008	tissue:retina\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf retina 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552008	GSM2552008: lrp2 mpf 1 mpf retina 12; Danio rerio; RNA Seq	GSM2552008		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552008	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAVRAAPEI-227_1.fq.gz	fastq	898471938.0	18336162.0	GSM2552008 r2	0:49 1:0	A:244766986;C:206211428;G:200463923;T:247021077;N:8524	49	0	244766986	206211428	200463923	247021077	8524	SRX2677131	SRS2075552	SRA549807	GEO	Medical College of Wisconsin	1	0.89516	0.16388	0.7064	0.4955	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42052	42052	SRR5382032	SRX2677130	SRS2075551	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf retina 11	GSM2552007	tissue:retina\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf retina 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552007	GSM2552007: lrp2 mpf 1 mpf retina 11; Danio rerio; RNA Seq	GSM2552007		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552007	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAURAAPEI-225_1.fq.gz	fastq	821148272.0	16758128.0	GSM2552007 r1	0:49 1:0	A:223278809;C:188723305;G:184465552;T:224674360;N:6246	49	0	223278809	188723305	184465552	224674360	6246	SRX2677130	SRS2075551	SRA549807	GEO	Medical College of Wisconsin	1	0.89197	0.15625	0.70502	0.48945	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42053	42053	SRR5382033	SRX2677130	SRS2075551	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf retina 11	GSM2552007	tissue:retina\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf retina 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552007	GSM2552007: lrp2 mpf 1 mpf retina 11; Danio rerio; RNA Seq	GSM2552007		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552007	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAURAAPEI-225_1.fq.gz	fastq	904858500.0	18466500.0	GSM2552007 r2	0:49 1:0	A:245787210;C:208119300;G:203490934;T:247452637;N:8419	49	0	245787210	208119300	203490934	247452637	8419	SRX2677130	SRS2075551	SRA549807	GEO	Medical College of Wisconsin	1	0.89893	0.15664	0.70382	0.49338	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42054	42054	SRR5382031	SRX2677129	SRS2075550	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf RPE 21	GSM2552006	tissue:retinal pigment epithelium\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf RPE 21	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552006	GSM2552006: lrp2 mpf 1 mpf RPE 21; Danio rerio; RNA Seq	GSM2552006		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552006	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150726_I114_FCH35J7BBXX_L7_HKZEBxagRBAARABPEI-220_1.fq.gz	fastq	1640688315.0	33483435.0	GSM2552006 r1	0:49 1:0	A:433572086;C:384856932;G:377705367;T:444542626;N:11304	49	0	433572086	384856932	377705367	444542626	11304	SRX2677129	SRS2075550	SRA549807	GEO	Medical College of Wisconsin	1	0.894	0.12185	0.68781	0.49822	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42055	42055	SRR5382029	SRX2677128	SRS2075549	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf RPE 13	GSM2552005	tissue:retinal pigment epithelium\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf RPE 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552005	GSM2552005: lrp2 mpf 1 mpf RPE 13; Danio rerio; RNA Seq	GSM2552005		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552005	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAQRAAPEI-220_1.fq.gz	fastq	676224157.0	13800493.0	GSM2552005 r1	0:49 1:0	A:180366332;C:156589454;G:154935435;T:182635962;N:1696974	49	0	180366332	156589454	154935435	182635962	1696974	SRX2677128	SRS2075549	SRA549807	GEO	Medical College of Wisconsin	1	0.89751	0.13119	0.69441	0.50128	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42056	42056	SRR5382030	SRX2677128	SRS2075549	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf RPE 13	GSM2552005	tissue:retinal pigment epithelium\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf RPE 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552005	GSM2552005: lrp2 mpf 1 mpf RPE 13; Danio rerio; RNA Seq	GSM2552005		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552005	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAQRAAPEI-220_1.fq.gz	fastq	801242267.0	16351883.0	GSM2552005 r2	0:49 1:0	A:214063611;C:186150617;G:184165214;T:216859021;N:3804	49	0	214063611	186150617	184165214	216859021	3804	SRX2677128	SRS2075549	SRA549807	GEO	Medical College of Wisconsin	1	0.9008	0.13185	0.69323	0.4968	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42057	42057	SRR5382027	SRX2677127	SRS2075548	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf RPE 12	GSM2552004	tissue:retinal pigment epithelium\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf RPE 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552004	GSM2552004: lrp2 mpf 1 mpf RPE 12; Danio rerio; RNA Seq	GSM2552004		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552004	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAPRAAPEI-219_1.fq.gz	fastq	661637837.0	13502813.0	GSM2552004 r1	0:49 1:0	A:176324364;C:153911375;G:151275995;T:178389637;N:1736466	49	0	176324364	153911375	151275995	178389637	1736466	SRX2677127	SRS2075548	SRA549807	GEO	Medical College of Wisconsin	1	0.89679	0.12464	0.68205	0.49183	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42058	42058	SRR5382028	SRX2677127	SRS2075548	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf RPE 12	GSM2552004	tissue:retinal pigment epithelium\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf RPE 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552004	GSM2552004: lrp2 mpf 1 mpf RPE 12; Danio rerio; RNA Seq	GSM2552004		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552004	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAPRAAPEI-219_1.fq.gz	fastq	771285088.0	15740512.0	GSM2552004 r2	0:49 1:0	A:205889481;C:180075876;G:176967027;T:208349042;N:3662	49	0	205889481	180075876	176967027	208349042	3662	SRX2677127	SRS2075548	SRA549807	GEO	Medical College of Wisconsin	1	0.89897	0.12535	0.68337	0.48697	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42059	42059	SRR5382025	SRX2677126	SRS2075547	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf eyes 3	GSM2552003	tissue:whole eyes\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf eyes 3	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552003	GSM2552003: lrp2 mpf 1 mpf eyes 3; Danio rerio; RNA Seq	GSM2552003		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552003	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAORAAPEI-218_1.fq.gz	fastq	723477454.0	14764846.0	GSM2552003 r1	0:49 1:0	A:192239117;C:170175036;G:165348255;T:193868733;N:1846313	49	0	192239117	170175036	165348255	193868733	1846313	SRX2677126	SRS2075547	SRA549807	GEO	Medical College of Wisconsin	1	0.90222	0.12773	0.68617	0.47685	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42060	42060	SRR5382026	SRX2677126	SRS2075547	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf eyes 3	GSM2552003	tissue:whole eyes\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf eyes 3	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552003	GSM2552003: lrp2 mpf 1 mpf eyes 3; Danio rerio; RNA Seq	GSM2552003		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552003	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAORAAPEI-218_1.fq.gz	fastq	849657746.0	17339954.0	GSM2552003 r2	0:49 1:0	A:226120997;C:200571753;G:194784071;T:228176838;N:4087	49	0	226120997	200571753	194784071	228176838	4087	SRX2677126	SRS2075547	SRA549807	GEO	Medical College of Wisconsin	1	0.90381	0.12659	0.68527	0.47307	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42061	42061	SRR5382023	SRX2677125	SRS2075546	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf eyes 2	GSM2552002	tissue:whole eyes\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf eyes 2	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552002	GSM2552002: lrp2 mpf 1 mpf eyes 2; Danio rerio; RNA Seq	GSM2552002		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552002	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAANRAAPEI-216_1.fq.gz	fastq	731986010.0	14938490.0	GSM2552002 r1	0:49 1:0	A:194148078;C:172782798;G:168124540;T:195035708;N:1894886	49	0	194148078	172782798	168124540	195035708	1894886	SRX2677125	SRS2075546	SRA549807	GEO	Medical College of Wisconsin	1	0.90549	0.10568	0.6884	0.476	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42062	42062	SRR5382024	SRX2677125	SRS2075546	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf eyes 2	GSM2552002	tissue:whole eyes\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf eyes 2	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552002	GSM2552002: lrp2 mpf 1 mpf eyes 2; Danio rerio; RNA Seq	GSM2552002		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552002	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAANRAAPEI-216_1.fq.gz	fastq	862250991.0	17596959.0	GSM2552002 r2	0:49 1:0	A:229099692;C:204203154;G:198695417;T:230248629;N:4099	49	0	229099692	204203154	198695417	230248629	4099	SRX2677125	SRS2075546	SRA549807	GEO	Medical College of Wisconsin	1	0.90837	0.10601	0.68903	0.45932	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42063	42063	SRR5382021	SRX2677124	SRS2075545	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf eyes 1	GSM2552001	tissue:whole eyes\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf eyes 1	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552001	GSM2552001: lrp2 mpf 1 mpf eyes 1; Danio rerio; RNA Seq	GSM2552001		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552001	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAMRAAPEI-214_1.fq.gz	fastq	869975253.0	17754597.0	GSM2552001 r1	0:49 1:0	A:229664008;C:206113797;G:200906294;T:231030590;N:2260564	49	0	229664008	206113797	200906294	231030590	2260564	SRX2677124	SRS2075545	SRA549807	GEO	Medical College of Wisconsin	1	0.90483	0.11515	0.68515	0.47313	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42064	42064	SRR5382022	SRX2677124	SRS2075545	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		lrp2 mpf 1 mpf eyes 1	GSM2552001	tissue:whole eyes\|genotype:lrp2 / \|age:1 mpf	lrp2 mpf 1 mpf eyes 1	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:lrp2 / \|age:1 mpf	GSM2552001	GSM2552001: lrp2 mpf 1 mpf eyes 1; Danio rerio; RNA Seq	GSM2552001		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552001	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAMRAAPEI-214_1.fq.gz	fastq	914727884.0	18667916.0	GSM2552001 r2	0:49 1:0	A:241918752;C:217461160;G:211918468;T:243425755;N:3749	49	0	241918752	217461160	211918468	243425755	3749	SRX2677124	SRS2075545	SRA549807	GEO	Medical College of Wisconsin	1	0.90759	0.11592	0.68505	0.48054	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42065	42065	SRR5382019	SRX2677123	SRS2075544	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf sclera 13	GSM2552000	tissue:choroid/sclera\|genotype:wild type\|age:1 mpf	ZDR 1 mpf sclera 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2552000	GSM2552000: ZDR 1 mpf sclera 13; Danio rerio; RNA Seq	GSM2552000		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552000	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAIRAAPEI-210_1.fq.gz	fastq	723705892.0	14769508.0	GSM2552000 r1	0:49 1:0	A:189459230;C:171808598;G:168845608;T:191709984;N:1882472	49	0	189459230	171808598	168845608	191709984	1882472	SRX2677123	SRS2075544	SRA549807	GEO	Medical College of Wisconsin	1	0.8885	0.08592	0.7093	0.46515	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42066	42066	SRR5382020	SRX2677123	SRS2075544	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf sclera 13	GSM2552000	tissue:choroid/sclera\|genotype:wild type\|age:1 mpf	ZDR 1 mpf sclera 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2552000	GSM2552000: ZDR 1 mpf sclera 13; Danio rerio; RNA Seq	GSM2552000		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552000	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAIRAAPEI-210_1.fq.gz	fastq	835178687.0	17044463.0	GSM2552000 r2	0:49 1:0	A:219032897;C:198915529;G:195473137;T:221752813;N:4311	49	0	219032897	198915529	195473137	221752813	4311	SRX2677123	SRS2075544	SRA549807	GEO	Medical College of Wisconsin	1	0.89282	0.08675	0.70767	0.46691	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42067	42067	SRR5382017	SRX2677122	SRS2075543	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf sclera 12	GSM2551999	tissue:choroid/sclera\|genotype:wild type\|age:1 mpf	ZDR 1 mpf sclera 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551999	GSM2551999: ZDR 1 mpf sclera 12; Danio rerio; RNA Seq	GSM2551999		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551999	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAHRAAPEI-209_1.fq.gz	fastq	720619774.0	14706526.0	GSM2551999 r1	0:49 1:0	A:189843421;C:170258398;G:165954852;T:192642877;N:1920226	49	0	189843421	170258398	165954852	192642877	1920226	SRX2677122	SRS2075543	SRA549807	GEO	Medical College of Wisconsin	1	0.88799	0.09077	0.69307	0.46834	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42068	42068	SRR5382018	SRX2677122	SRS2075543	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf sclera 12	GSM2551999	tissue:choroid/sclera\|genotype:wild type\|age:1 mpf	ZDR 1 mpf sclera 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551999	GSM2551999: ZDR 1 mpf sclera 12; Danio rerio; RNA Seq	GSM2551999		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551999	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAHRAAPEI-209_1.fq.gz	fastq	814612652.0	16624748.0	GSM2551999 r2	0:49 1:0	A:215000926;C:193099554;G:188185253;T:218322960;N:3959	49	0	215000926	193099554	188185253	218322960	3959	SRX2677122	SRS2075543	SRA549807	GEO	Medical College of Wisconsin	1	0.89194	0.09267	0.69345	0.47187	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42069	42069	SRR5382015	SRX2677121	SRS2075542	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf sclera 11	GSM2551998	tissue:choroid/sclera\|genotype:wild type\|age:1 mpf	ZDR 1 mpf sclera 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551998	GSM2551998: ZDR 1 mpf sclera 11; Danio rerio; RNA Seq	GSM2551998		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551998	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAGRAAPEI-208_1.fq.gz	fastq	711301150.0	14516350.0	GSM2551998 r1	0:49 1:0	A:187610754;C:167656660;G:164414397;T:189785378;N:1833961	49	0	187610754	167656660	164414397	189785378	1833961	SRX2677121	SRS2075542	SRA549807	GEO	Medical College of Wisconsin	1	0.89019	0.08546	0.71112	0.46026	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42070	42070	SRR5382016	SRX2677121	SRS2075542	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf sclera 11	GSM2551998	tissue:choroid/sclera\|genotype:wild type\|age:1 mpf	ZDR 1 mpf sclera 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	choroid/sclera		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551998	GSM2551998: ZDR 1 mpf sclera 11; Danio rerio; RNA Seq	GSM2551998		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551998	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAGRAAPEI-208_1.fq.gz	fastq	812115073.0	16573777.0	GSM2551998 r2	0:49 1:0	A:214551124;C:192083365;G:188317025;T:217159406;N:4153	49	0	214551124	192083365	188317025	217159406	4153	SRX2677121	SRS2075542	SRA549807	GEO	Medical College of Wisconsin	1	0.89273	0.08561	0.71151	0.46434	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42071	42071	SRR5382013	SRX2677120	SRS2075541	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf retina 13	GSM2551997	tissue:retina\|genotype:wild type\|age:1 mpf	ZDR 1 mpf retina 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551997	GSM2551997: ZDR 1 mpf retina 13; Danio rerio; RNA Seq	GSM2551997		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551997	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAALRAAPEI-213_1.fq.gz	fastq	627516148.0	12806452.0	GSM2551997 r1	0:49 1:0	A:170179227;C:144206894;G:141003173;T:170495840;N:1631014	49	0	170179227	144206894	141003173	170495840	1631014	SRX2677120	SRS2075541	SRA549807	GEO	Medical College of Wisconsin	1	0.87699	0.15658	0.70853	0.4864	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42072	42072	SRR5382014	SRX2677120	SRS2075541	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf retina 13	GSM2551997	tissue:retina\|genotype:wild type\|age:1 mpf	ZDR 1 mpf retina 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551997	GSM2551997: ZDR 1 mpf retina 13; Danio rerio; RNA Seq	GSM2551997		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551997	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAALRAAPEI-213_1.fq.gz	fastq	728730597.0	14872053.0	GSM2551997 r2	0:49 1:0	A:197954872;C:168023610;G:164244521;T:198504024;N:3570	49	0	197954872	168023610	164244521	198504024	3570	SRX2677120	SRS2075541	SRA549807	GEO	Medical College of Wisconsin	1	0.88024	0.15744	0.70798	0.4864	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42073	42073	SRR5382011	SRX2677119	SRS2075540	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf retina 12	GSM2551996	tissue:retina\|genotype:wild type\|age:1 mpf	ZDR 1 mpf retina 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551996	GSM2551996: ZDR 1 mpf retina 12; Danio rerio; RNA Seq	GSM2551996		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551996	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAKRAAPEI-212_1.fq.gz	fastq	750179269.0	15309781.0	GSM2551996 r1	0:49 1:0	A:202189760;C:173630838;G:168978527;T:203409292;N:1970852	49	0	202189760	173630838	168978527	203409292	1970852	SRX2677119	SRS2075540	SRA549807	GEO	Medical College of Wisconsin	1	0.88077	0.14126	0.70589	0.49134	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42074	42074	SRR5382012	SRX2677119	SRS2075540	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf retina 12	GSM2551996	tissue:retina\|genotype:wild type\|age:1 mpf	ZDR 1 mpf retina 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551996	GSM2551996: ZDR 1 mpf retina 12; Danio rerio; RNA Seq	GSM2551996		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551996	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAKRAAPEI-212_1.fq.gz	fastq	897558088.0	18317512.0	GSM2551996 r2	0:49 1:0	A:242294855;C:208492061;G:202846754;T:243920033;N:4385	49	0	242294855	208492061	202846754	243920033	4385	SRX2677119	SRS2075540	SRA549807	GEO	Medical College of Wisconsin	1	0.8857	0.14195	0.70536	0.48882	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42075	42075	SRR5382009	SRX2677118	SRS2075539	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf retina 11	GSM2551995	tissue:retina\|genotype:wild type\|age:1 mpf	ZDR 1 mpf retina 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551995	GSM2551995: ZDR 1 mpf retina 11; Danio rerio; RNA Seq	GSM2551995		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551995	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAJRAAPEI-211_1.fq.gz	fastq	823785942.0	16811958.0	GSM2551995 r1	0:49 1:0	A:222797674;C:189722377;G:184455267;T:224717827;N:2092797	49	0	222797674	189722377	184455267	224717827	2092797	SRX2677118	SRS2075539	SRA549807	GEO	Medical College of Wisconsin	1	0.87839	0.15243	0.70987	0.49087	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42076	42076	SRR5382010	SRX2677118	SRS2075539	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf retina 11	GSM2551995	tissue:retina\|genotype:wild type\|age:1 mpf	ZDR 1 mpf retina 11	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retina		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551995	GSM2551995: ZDR 1 mpf retina 11; Danio rerio; RNA Seq	GSM2551995		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551995	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAJRAAPEI-211_1.fq.gz	fastq	915019826.0	18673874.0	GSM2551995 r2	0:49 1:0	A:247862749;C:211485352;G:205487891;T:250180081;N:3753	49	0	247862749	211485352	205487891	250180081	3753	SRX2677118	SRS2075539	SRA549807	GEO	Medical College of Wisconsin	1	0.88022	0.1533	0.71023	0.4871	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42077	42077	SRR5382007	SRX2677117	SRS2075538	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf RPE 13	GSM2551994	tissue:retinal pigment epithelium\|genotype:wild type\|age:1 mpf	ZDR 1 mpf RPE 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551994	GSM2551994: ZDR 1 mpf RPE 13; Danio rerio; RNA Seq	GSM2551994		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551994	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAFRAAPEI-207_1.fq.gz	fastq	638481025.0	13030225.0	GSM2551994 r1	0:49 1:0	A:169350435;C:149047615;G:147980872;T:170459893;N:1642210	49	0	169350435	149047615	147980872	170459893	1642210	SRX2677117	SRS2075538	SRA549807	GEO	Medical College of Wisconsin	1	0.89027	0.11552	0.69268	0.47791	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42078	42078	SRR5382008	SRX2677117	SRS2075538	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf RPE 13	GSM2551994	tissue:retinal pigment epithelium\|genotype:wild type\|age:1 mpf	ZDR 1 mpf RPE 13	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551994	GSM2551994: ZDR 1 mpf RPE 13; Danio rerio; RNA Seq	GSM2551994		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551994	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAFRAAPEI-207_1.fq.gz	fastq	753109420.0	15369580.0	GSM2551994 r2	0:49 1:0	A:200026171;C:176448366;G:175132341;T:201498888;N:3654	49	0	200026171	176448366	175132341	201498888	3654	SRX2677117	SRS2075538	SRA549807	GEO	Medical College of Wisconsin	1	0.89342	0.1153	0.69301	0.47451	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42079	42079	SRR5382005	SRX2677116	SRS2075537	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf RPE 12	GSM2551993	tissue:retinal pigment epithelium\|genotype:wild type\|age:1 mpf	ZDR 1 mpf RPE 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551993	GSM2551993: ZDR 1 mpf RPE 12; Danio rerio; RNA Seq	GSM2551993		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551993	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAERAAPEI-206_1.fq.gz	fastq	711158756.0	14513444.0	GSM2551993 r1	0:49 1:0	A:190423173;C:164563930;G:162474409;T:191835770;N:1861474	49	0	190423173	164563930	162474409	191835770	1861474	SRX2677116	SRS2075537	SRA549807	GEO	Medical College of Wisconsin	1	0.88325	0.12011	0.69913	0.49648	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	Eye	Sensory System
42080	42080	SRR5382006	SRX2677116	SRS2075537	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf		ZDR 1 mpf RPE 12	GSM2551993	tissue:retinal pigment epithelium\|genotype:wild type\|age:1 mpf	ZDR 1 mpf RPE 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	retinal pigment epithelium		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:1 mpf	GSM2551993	GSM2551993: ZDR 1 mpf RPE 12; Danio rerio; RNA Seq	GSM2551993		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2551993	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAERAAPEI-206_1.fq.gz	fastq	822460884.0	16784916.0	GSM2551993 r2	0:49 1:0	A:220616018;C:191013675;G:188473709;T:222353408;N:4074	49	0	220616018	191013675	188473709	222353408	4074	SRX2677116	SRS2075537	SRA549807	GEO	Medical College of Wisconsin	1	0.88727	0.11911	0.69777	0.48971	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-03-28	Juvenile	Juvenile	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");;