{"database": "metadata", "table": "run_metadata", "rows": [[9824, "ERR3957798", "ERX3965602", "ERS4355885", "ERP120207", "PRJEB36940", "RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls", "E-MTAB-8824", "Transcriptome Analysis", "Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose  redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4  FBLN5  LTBP4 and ELN  encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1  ATP6V1A  ATP6V0A2  ALDH18A1  RIN2  GORAB  PYCR1 and SLC2A10. ATP6V1E1\u2013related CL cause loose redundant skin folds  variable mental disability  typical facial characteristics  lipodystrophy  hypotonia  and cardiopulmonary involvement including pneumothorax  hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up  or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis  we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b  disrupting transcription atp6v1e1bhi577aTg/+  from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b  c.334insGG; c.337 340delCGG  predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis.   Overview of the experimental work flow:   Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later   RNA extraction: TRIzol\u00ae Reagent RNeasy mini kit Qiagen according to manufacturer's instructions   RNA integrity: 2100 Bioanalyzer Agilent   Sequencing library: TruSeq\u00ae Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq\u00ae RNA Single Indexes Set A Illumina   Sequencing: HiSeq 3000 sequencer Illumina   paired end 150 bp   sequencing facility of the Center of Medical Genetics Ghent   alignement to zebrafish GRCz10 reference genome to generate bam files    RNA seq pipeline was used that was published by the nf core community. This pipeline was executed using the Nextflow engine for computational workflows and comprises several processing steps. QC analysis of the RNA seq data was performed with FastQC and MultiQC. TrimGalore was used to remove adapter contamination and to trim low quality regions. Duplicate reads were identified with MarkDuplicates. Subsequently  all cleaned and trimmed reads that passed QC were aligned to GRCz10 using STAR aligner. Gene counts were computed using the featureCounts package. Differential expression analysis subsequently was performed on these gene counts using DESeq2. Differentially expressed genes were identified using a fold change cut off >1 and FDR=0.05. Finally  GO enrichment & pathway analysis were performed on differentially expressed gene sets using the Generally Applicable Gene set Enrichment for Pathway Analysis GAGE algorithm.", "ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26", null, "Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol\u00ae Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq\u00ae Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq\u00ae RNA Single Indexes Set A Illumina.", "atp6v1e1b +/+ 1", "SAMEA6591591", "Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University", "ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:53Z|External Id:SAMEA6591591|INSDC center name:Center for Medical Genetics Ghent  Ghent University Hospital  Ghent  Belgium Department of biomolecular medicine  Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:53Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b +/+ 1|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:normal|genotype:atp6v1e1b +/+|individual:pool of 10 larvae|organism part:whole organism|phenotype:wild type|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b +/+ 1|scientific name:Danio rerio|sex:male|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls", "E MTAB 8824:atp6v1e1b +/+ 1 p", "atp6v1e1b +/+ 1 p", "RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls", "Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol\u00ae Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq\u00ae Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq\u00ae RNA Single Indexes Set A Illumina.", "Experimental Factor: genotype:atp6v1e1b +/+|Experimental Factor: disease:normal", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP120207", "Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls", "ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26", "atp6v1e1b_wt_1_R1.fastq.gz atp6v1e1b_wt_1_R2.fastq.gz", "fastq fastq", 12570351660.0, 42959340.0, "E MTAB 8824:atp6v1e1b wt 1 R", "0:146.34 1:146.27", "A:3284633072;C:2995010895;G:2959080366;T:3328876226;N:2751101", 146, 146, null, null, 3284633072, 2995010895, 2959080366, 3328876226, 2751101, "ERX3965602", "ERS4355885", "ERA2393549", "Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive", "Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive", 2, 0.95027, 0.95086, 0.06766, 0.06493, 0.66667, 0.6747, 0.46208, 0.46879, 150, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2020-02-26", "Larval", "Larval", "Whole Organism", "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": ["9824"], "units": {}, "query_ms": 11.136793997138739}