{"database": "metadata", "table": "run_metadata", "rows": [[41874, "SRR5320504", "SRX2619909", "SRS2029872", "SRP101556", "PRJNA378487", "Transcriptional profiling of the zebrafish proximal tubule", "GSE95808", "Transcriptome Analysis", "The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue", null, "pubmed:31188030", null, "Morpholino 5", "GSM2526319", null, "tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "Morpholino 5", "Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.", "larval kidney", null, "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", null, "line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "GSM2526319", "GSM2526319: Morpholino 5; Danio rerio; RNA Seq", "GSM2526319", null, "1", "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", "GEO Accession:GSM2526319", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101556", null, null, "C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R1_001.fastq.gz C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R2_001.fastq.gz", "fastq fastq", 9864273500.0, 39457094.0, "GSM2526319 r1", "0:125 1:125", "A:2628741477;C:2304848464;G:2364915536;T:2562525014;N:3243009", 125, 125, null, null, 2628741477, 2304848464, 2364915536, 2562525014, 3243009, "SRX2619909", "SRS2029872", "SRA543390", "GEO", "Molecular Medicine and Pathology, University of Auckland", 2, 0.96115, 0.96161, 0.10876, 0.10854, 0.67495, 0.67616, 0.45304, 0.45767, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "New Zealand", "2017-03-08", "Multi-stage", "Multi-stage", "Kidney", "Renal 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": ["41874"], "units": {}, "query_ms": 13.31182100057049}