{"database": "metadata", "table": "run_metadata", "rows": [[62006, "SRR13115082", "SRX9557295", "SRS7772891", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNI130317 D3 5", "GSM4930054", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf", "ZNI130317 D3 5", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf", "GSM4930054", "GSM4930054: ZNI130317 D3 5; Danio rerio; RNA Seq", "GSM4930054", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930054", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNI130317_D3_5_R1.fastq.gz ZNI130317_D3_5_R2.fastq.gz", "fastq fastq", 370600.0, 3706.0, "GSM4930054 r1", "0:30 1:70", "A:103174;C:82663;G:82368;T:102335;N:60", 30, 70, null, null, 103174, 82663, 82368, 102335, 60, "SRX9557295", "SRS7772891", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.00286, 0.00114, 0.00285, 0.00085, 1.0, 0.99997, null, 1.0, 30, 70, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"]], "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": ["62006"], "units": {}, "query_ms": 9.1622290055966}