run_metadata: 42021

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
42021	SRR5382065	SRX2677146	SRS2075567	SRP102601	PRJNA380770	Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error	GSE97125	Transcriptome Analysis	We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf				NO shh 12	GSM2552023		tissue:whole larval eyes\|genotype:wild type\|age:5 dpf	NO shh 12	Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.	whole larval eyes		Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet	genotype:wild type\|age:5 dpf	GSM2552023	GSM2552023: NO shh 12; Danio rerio; RNA Seq	GSM2552023		1	Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.	GEO Accession:GSM2552023	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP102601			150627_I114_FCH2TT2BBXX_L7_HKZEBxagRABGRAAPEI-212_1.fq.gz	fastq	834811089.0	17036961.0	GSM2552023 r2	0:49 1:0	A:219382137;C:199232543;G:192142641;T:224045481;N:8287	49	0			219382137	199232543	192142641	224045481	8287	SRX2677146	SRS2075567	SRA549807	GEO	Medical College of Wisconsin	1	0.90899		0.11358		0.68809		0.43149		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2017-03-28	Larval	Larval	Eye	Sensory System