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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
9819 ERR3957803 ERX3965607 ERS4355890 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–related 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® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® 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   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® 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® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b cmg78/cmg78 3 SAMEA6591596 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 26T13:29:54Z|External Id:SAMEA6591596|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 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b cmg78/cmg78 3|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:gene knock out|genotype:atp6v1e1b cmg78/cmg78|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b cmg78/cmg78 3|scientific name:Danio rerio|sex:male|strain:AB                 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 cmg78/cmg78 3 p atp6v1e1b cmg78/cmg78 3 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® 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® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b cmg78/cmg78|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   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_cmg78cmg78_3_R1.fastq.gz atp6v1e1b_cmg78cmg78_3_R2.fastq.gz fastq fastq 11394931126.0 38868508.0 E MTAB 8824:atp6v1e1b cmg78cmg78 3 R 0:146.62 1:146.54 A:2997347418;C:2691952662;G:2671891078;T:3032072506;N:1667462 146 146     2997347418 2691952662 2671891078 3032072506 1667462 ERX3965607 ERS4355890 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 0.94663 0.94787 0.07048 0.0672 0.66444 0.67105 0.46855 0.46335 151 150 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures