{"database": "metadata", "table": "run_metadata", "rows": [[42040, "SRR5382044", "SRX2677136", "SRS2075557", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf", null, null, null, "bmp4 11", "GSM2552013", null, "tissue:whole larval eyes|genotype:Transgenic hsp70l:eGFP bmp4|age:5 dpf", "bmp4 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole larval eyes", null, "Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet", "genotype:Transgenic hsp70l:eGFP bmp4|age:5 dpf", "GSM2552013", "GSM2552013: bmp4 11; Danio rerio; RNA Seq", "GSM2552013", null, "1", "Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552013", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAXRAAPEI-202_1.fq.gz", "fastq", 818072248.0, 16695352.0, "GSM2552013 r1", "0:49 1:0", "A:213364768;C:196897651;G:191539621;T:216263952;N:6256", 49, 0, null, null, 213364768, 196897651, 191539621, 216263952, 6256, "SRX2677136", "SRS2075557", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89563, null, 0.10696, null, 0.68828, null, 0.44425, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Larval", "Larval", "Eye", "Sensory System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["42040"], "units": {}, "query_ms": 11.726019998604897}