metadata: run_metadata: 59 rows where devstage_curation_coarse = "Juvenile" and tissue_curation

59 rows where devstage_curation_coarse = "Juvenile" 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.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	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.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
42081	42081	SRR5382003	SRX2677115	SRS2075536	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 11	GSM2551992	tissue:retinal pigment epithelium\|genotype:wild type\|age:1 mpf	ZDR 1 mpf RPE 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.	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	GSM2551992	GSM2551992: ZDR 1 mpf RPE 11; Danio rerio; RNA Seq	GSM2551992		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:GSM2551992	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAADRAAPEI-205_1.fq.gz	fastq	760825107.0	15527043.0	GSM2551992 r1	0:49 1:0	A:203332989;C:175754207;G:174105427;T:205609497;N:2022987	49	0	203332989	175754207	174105427	205609497	2022987	SRX2677115	SRS2075536	SRA549807	GEO	Medical College of Wisconsin	1	0.88248		0.11721		0.69398		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
42082	42082	SRR5382004	SRX2677115	SRS2075536	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 11	GSM2551992	tissue:retinal pigment epithelium\|genotype:wild type\|age:1 mpf	ZDR 1 mpf RPE 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.	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	GSM2551992	GSM2551992: ZDR 1 mpf RPE 11; Danio rerio; RNA Seq	GSM2551992		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:GSM2551992	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAADRAAPEI-205_1.fq.gz	fastq	839301057.0	17128593.0	GSM2551992 r2	0:49 1:0	A:224733625;C:194508202;G:192706180;T:227349310;N:3740	49	0	224733625	194508202	192706180	227349310	3740	SRX2677115	SRS2075536	SRA549807	GEO	Medical College of Wisconsin	1	0.88552		0.11818		0.69392		0.48632		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
42083	42083	SRR5382001	SRX2677114	SRS2075535	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 eyes 3	GSM2551991	tissue:whole eyes\|genotype:wild type\|age:1 mpf	ZDR 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:wild type\|age:1 mpf	GSM2551991	GSM2551991: ZDR 1 mpf eyes 3; Danio rerio; RNA Seq	GSM2551991		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:GSM2551991	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAACRAAPEI-203_1.fq.gz	fastq	736025815.0	15020935.0	GSM2551991 r1	0:49 1:0	A:196052955;C:172994773;G:168209012;T:196847875;N:1921200	49	0	196052955	172994773	168209012	196847875	1921200	SRX2677114	SRS2075535	SRA549807	GEO	Medical College of Wisconsin	1	0.89497		0.11257		0.68852		0.47383		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
42084	42084	SRR5382002	SRX2677114	SRS2075535	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 eyes 3	GSM2551991	tissue:whole eyes\|genotype:wild type\|age:1 mpf	ZDR 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:wild type\|age:1 mpf	GSM2551991	GSM2551991: ZDR 1 mpf eyes 3; Danio rerio; RNA Seq	GSM2551991		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:GSM2551991	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAACRAAPEI-203_1.fq.gz	fastq	848026487.0	17306663.0	GSM2551991 r2	0:49 1:0	A:226256521;C:199987000;G:194486401;T:227292463;N:4102	49	0	226256521	199987000	194486401	227292463	4102	SRX2677114	SRS2075535	SRA549807	GEO	Medical College of Wisconsin	1	0.89861		0.11296		0.68836		0.46508		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
42085	42085	SRR5381999	SRX2677113	SRS2075534	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 eyes 2	GSM2551990	tissue:whole eyes\|genotype:wild type\|age:1 mpf	ZDR 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:wild type\|age:1 mpf	GSM2551990	GSM2551990: ZDR 1 mpf eyes 2; Danio rerio; RNA Seq	GSM2551990		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:GSM2551990	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAABRAAPEI-202_1.fq.gz	fastq	802949770.0	16386730.0	GSM2551990 r1	0:49 1:0	A:213127526;C:188823533;G:184394258;T:214490681;N:2113772	49	0	213127526	188823533	184394258	214490681	2113772	SRX2677113	SRS2075534	SRA549807	GEO	Medical College of Wisconsin	1	0.89543		0.10967		0.69209		0.47916		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
42086	42086	SRR5382000	SRX2677113	SRS2075534	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 eyes 2	GSM2551990	tissue:whole eyes\|genotype:wild type\|age:1 mpf	ZDR 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:wild type\|age:1 mpf	GSM2551990	GSM2551990: ZDR 1 mpf eyes 2; Danio rerio; RNA Seq	GSM2551990		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:GSM2551990	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAABRAAPEI-202_1.fq.gz	fastq	914629639.0	18665911.0	GSM2551990 r2	0:49 1:0	A:243198380;C:215821497;G:210710354;T:244895308;N:4100	49	0	243198380	215821497	210710354	244895308	4100	SRX2677113	SRS2075534	SRA549807	GEO	Medical College of Wisconsin	1	0.89876		0.11007		0.69467		0.47115		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
42087	42087	SRR5381997	SRX2677112	SRS2075533	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 eyes 1	GSM2551989	tissue:whole eyes\|genotype:wild type\|age:1 mpf	ZDR 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:wild type\|age:1 mpf	GSM2551989	GSM2551989: ZDR 1 mpf eyes 1; Danio rerio; RNA Seq	GSM2551989		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:GSM2551989	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAARAAPEI-201_1.fq.gz	fastq	786951466.0	16060234.0	GSM2551989 r1	0:49 1:0	A:206839376;C:187666900;G:181310367;T:209045476;N:2089347	49	0	206839376	187666900	181310367	209045476	2089347	SRX2677112	SRS2075533	SRA549807	GEO	Medical College of Wisconsin	1	0.89138		0.10868		0.68943		0.45278		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
42088	42088	SRR5381998	SRX2677112	SRS2075533	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 eyes 1	GSM2551989	tissue:whole eyes\|genotype:wild type\|age:1 mpf	ZDR 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:wild type\|age:1 mpf	GSM2551989	GSM2551989: ZDR 1 mpf eyes 1; Danio rerio; RNA Seq	GSM2551989		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:GSM2551989	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP102601	150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAARAAPEI-201_1.fq.gz	fastq	914454317.0	18662333.0	GSM2551989 r2	0:49 1:0	A:240676436;C:218930366;G:211397133;T:243446328;N:4054	49	0	240676436	218930366	211397133	243446328	4054	SRX2677112	SRS2075533	SRA549807	GEO	Medical College of Wisconsin	1	0.89338		0.10969		0.69163		0.46453		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
61643	61643	SRR12899696	SRX9364743	SRS7586958	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	nrl R2	GSM4861209	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf KO	nrl R2	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf KO	GSM4861209	GSM4861209: nrl R2; Danio rerio; RNA Seq	GSM4861209		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861209	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615	nrl-R2_combined_R1.fastq.gz nrl-R2_combined_R2.fastq.gz	fastq fastq	7231497600.0	24104992.0	GSM4861209 r1	0:150 1:150	A:1995457626;C:1613822880;G:1630032692;T:1991951852;N:232550	150	150	1995457626	1613822880	1630032692	1991951852	232550	SRX9364743	SRS7586958	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.91539	0.91383	0.13441	0.13499	0.69296	0.70021	0.5139	0.50426	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
61644	61644	SRR12899695	SRX9364742	SRS7586957	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	nrl R1	GSM4861208	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf KO	nrl R1	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf KO	GSM4861208	GSM4861208: nrl R1; Danio rerio; RNA Seq	GSM4861208		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861208	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615	nrl-R1_combined_R1.fastq.gz nrl-R1_combined_R2.fastq.gz	fastq fastq	6989998200.0	23299994.0	GSM4861208 r1	0:150 1:150	A:1947895730;C:1539849390;G:1551787456;T:1950215842;N:249782	150	150	1947895730	1539849390	1551787456	1950215842	249782	SRX9364742	SRS7586957	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.90616	0.9059	0.15209	0.15341	0.68998	0.69885	0.49879	0.49931	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
61645	61645	SRR12899694	SRX9364741	SRS7586956	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	WT R2	GSM4861207	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf type	WT R2	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf type	GSM4861207	GSM4861207: WT R2; Danio rerio; RNA Seq	GSM4861207		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861207	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615	WT-R2_combined_R1.fastq.gz WT-R2_combined_R2.fastq.gz	fastq fastq	7066558200.0	23555194.0	GSM4861207 r1	0:150 1:150	A:1911018201;C:1615965707;G:1630234641;T:1909071420;N:268231	150	150	1911018201	1615965707	1630234641	1909071420	268231	SRX9364741	SRS7586956	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.91673	0.91647	0.11542	0.11684	0.68781	0.69637	0.48784	0.49134	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
61646	61646	SRR12899693	SRX9364740	SRS7586955	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	WT R1	GSM4861206	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf type	WT R1	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf type	GSM4861206	GSM4861206: WT R1; Danio rerio; RNA Seq	GSM4861206		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861206	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615	WT-R1_combined_R1.fastq.gz WT-R1_combined_R2.fastq.gz	fastq fastq	6933407700.0	23111359.0	GSM4861206 r1	0:150 1:150	A:1917552178;C:1542500715;G:1553125711;T:1919988847;N:240249	150	150	1917552178	1542500715	1553125711	1919988847	240249	SRX9364740	SRS7586955	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.90701	0.90456	0.14405	0.14325	0.68335	0.69221	0.49207	0.4926	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
67572	67572	SRR17224783	SRX13404158	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye	breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal								RNAseq of zebrafish	eye mut 1 30dpf	eye mut 1 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669	eye_mut_1_30dpf.R1.fastq.gz eye_mut_1_30dpf.R2.fastq.gz	fastq fastq	6647236232.0	22010716.0	eye mut 1 30dpf.R1.fastq.gz	0:151 1:151	A:1828748374;C:1496039359;G:1520471614;T:1801966254;N:10631	151	151	1828748374	1496039359	1520471614	1801966254	10631	SRX13404158	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.91773	0.91812	0.11227	0.11178	0.6687	0.66931	0.47877	0.47805	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67573	67573	SRR17224784	SRX13404157	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye	breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal								RNAseq of zebrafish	eye wt 3 30dpf	eye wt 3 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669	eye_wt_3_30dpf.R1.fastq.gz eye_wt_3_30dpf.R2.fastq.gz	fastq fastq	6665043964.0	22069682.0	eye wt 3 30dpf.R1.fastq.gz	0:151 1:151	A:1837907813;C:1496332954;G:1517206099;T:1813585697;N:11401	151	151	1837907813	1496332954	1517206099	1813585697	11401	SRX13404157	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92328	0.92376	0.11972	0.11905	0.69002	0.69039	0.48654	0.48588	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67574	67574	SRR17224785	SRX13404156	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye	breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal								RNAseq of zebrafish	eye wt 2 30dpf	eye wt 2 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669	eye_wt_2_30dpf.R1.fastq.gz eye_wt_2_30dpf.R2.fastq.gz	fastq fastq	7313252536.0	24216068.0	eye wt 2 30dpf.R1.fastq.gz	0:151 1:151	A:2005760880;C:1644712229;G:1691008059;T:1971759242;N:12126	151	151	2005760880	1644712229	1691008059	1971759242	12126	SRX13404156	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92458	0.92267	0.11276	0.11098	0.68834	0.6939	0.48994	0.48977	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67575	67575	SRR17224786	SRX13404155	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye	breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal								RNAseq of zebrafish	eye wt 1 30dpf	eye wt 1 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669	eye_wt_1_30dpf.R1.fastq.gz eye_wt_1_30dpf.R2.fastq.gz	fastq fastq	7374231470.0	24417985.0	eye wt 1 30dpf.R1.fastq.gz	0:151 1:151	A:2032283041;C:1657026689;G:1681898985;T:2003011689;N:11066	151	151	2032283041	1657026689	1681898985	2003011689	11066	SRX13404155	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92217	0.92217	0.11433	0.11344	0.69045	0.69087	0.48935	0.47534	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67580	67580	SRR17224791	SRX13404150	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye	breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal								RNAseq of zebrafish	eye mut 3 30dpf	eye mut 3 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669	eye_mut_3_30dpf.R1.fastq.gz eye_mut_3_30dpf.R2.fastq.gz	fastq fastq	7370863566.0	24406833.0	eye mut 3 30dpf.R1.fastq.gz	0:151 1:151	A:2035593457;C:1650415961;G:1678944830;T:2005897248;N:12070	151	151	2035593457	1650415961	1678944830	2005897248	12070	SRX13404150	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.9169	0.91717	0.11546	0.11616	0.66249	0.66312	0.47895	0.47697	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67581	67581	SRR17224792	SRX13404149	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye	breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal								RNAseq of zebrafish	eye mut 2 30dpf	eye mut 2 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669	eye_mut_2_30dpf.R1.fastq.gz eye_mut_2_30dpf.R2.fastq.gz	fastq fastq	6025971496.0	19953548.0	eye mut 2 30dpf.R1.fastq.gz	0:151 1:151	A:1659612510;C:1355527081;G:1377376165;T:1633446020;N:9720	151	151	1659612510	1355527081	1377376165	1633446020	9720	SRX13404149	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.91909	0.92042	0.11187	0.11181	0.66884	0.66985	0.48856	0.49166	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
74633	74633	SRR23884658	SRX19696514	SRS17065387	SRP427793	PRJNA945580	Danio rerio strain:AB Raw sequence reads	PRJNA945580	Other	The Raw sequence reads of WT and miR 184 KO zebrafish eyes				210508902	strain:AB\|age:2 month\|sex:pooled male and female\|tissue:eyes\|ID:2\|BioSampleModel:Model organism or animal								WT 2	210508902	210508902	NEBNext Ultra RNA Library Prep Kit for Illumina			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 1000	SRP427793	WT_2_1.fq.gz WT_2_2.fq.gz	fastq fastq	6735894000.0	22452980.0	WT 2 1.fq.gz	0:150 1:150	A:1829468826;C:1562022082;G:1548721920;T:1795640273;N:40899	150	150	1829468826	1562022082	1548721920	1795640273	40899	SRX19696514	SRS17065387	SRA1605997	Henan university\|Joint National Laboratory for Antibody Drug Engine	Henan university	2	0.94008	0.9398	0.10958	0.11001	0.69907	0.70088	0.46448	0.46026	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2023-03-17	Juvenile	Juvenile	Eye	Sensory System
74634	74634	SRR23884659	SRX19696513	SRS17065384	SRP427793	PRJNA945580	Danio rerio strain:AB Raw sequence reads	PRJNA945580	Other	The Raw sequence reads of WT and miR 184 KO zebrafish eyes				210508901	strain:AB\|age:1 month\|sex:pooled male and female\|tissue:eyes\|ID:1\|BioSampleModel:Model organism or animal								WT 1	210508901	210508901	NEBNext Ultra RNA Library Prep Kit for Illumina			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 1000	SRP427793	WT_1_1.fq.gz WT_1_2.fq.gz	fastq fastq	6733134600.0	22443782.0	WT 1 1.fq.gz	0:150 1:150	A:1819908990;C:1568144240;G:1555637420;T:1789402357;N:41593	150	150	1819908990	1568144240	1555637420	1789402357	41593	SRX19696513	SRS17065384	SRA1605997	Henan university\|Joint National Laboratory for Antibody Drug Engine	Henan university	2	0.94058	0.94013	0.10559	0.10527	0.69676	0.69627	0.46962	0.46888	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2023-03-17	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");;