{"database": "metadata", "table": "run_metadata", "rows": [[56870, "SRR11140709", "SRX7777132", "SRS6196090", "SRP250312", "PRJNA607984", "Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy zebrafish", "GSE145711", "Transcriptome Analysis", "Intellectual disability ID is a heterogeneous clinical entity and includes an excess of males who harbor variants on the X chromosome XLID. We report rare FAM50A missense variants in the original Armfield XLID syndrome family localized in Xq28 and four additional unrelated males with overlapping features. Our fam50a knockout KO zebrafish model exhibits abnormal neurogenesis and craniofacial patterning  and in vivo complementation assays indicate that the patient derived variants are hypomorphic. RNA sequencing analysis from fam50a KO zebrafish show dysregulation of the transcriptome  with augmented spliceosome mRNAs and depletion of transcripts involved in neurodevelopment. Zebrafish RNA seq datasets show a preponderance of three prime alternative splicing events in fam50a KO  suggesting a role in the spliceosome C complex. These data are supported with transcriptomic signatures from cell lines derived from affected individuals and FAM50A protein protein interaction data. In sum  Armfield XLID syndrome is a spliceosomopathy associated with aberrant mRNA processing during development. Overall design: To investigate the impact of fam50a dysfunction in an in vivo neurodevelopmental context  we performed transcriptomics studies using RNA isolated from heads of fam50a CRISPR KO and wild type zebrafish larvae at 2 dpf five biological replicates each", null, "pubmed:32703943", null, "KK S2", "GSM4331445", null, "tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf type", "KK S2", "RNA seq data were processed using the TrimGalore toolkit http://www.bioinformatics.babraham.ac.uk/projects/trim galore which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3\u2019 end of reads. Only reads that were 20 nt or longer post trimming were kept for further analysis. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool and retained for subsequent analysis if they mapped to a single genomic location. Gene counts were compiled using the HTSeq tool http://www huber.embl.de/users/anders/HTSeq/  and only genes that had \u226510 reads in any given library were used in subsequent analyses. Normalization and differential expression were carried out using the DESeq2 Bioconductor package with the R statistical programming environment www.r project.org. False discovery rate was calculated to control for multiple hypothesis testing. Gene set enrichment analysis was performed to identify gene ontology terms associated with altered gene expression for each comparison. Alternative splicing was characterized using the rMATS algorithm  which employs the STAR alignment tool along with the Zv10r87 version of the zebrafish genome and transcriptome. DAVID pathway analysis was run on significant genes FDR <= 5% on each of the five alternative splicing event categories as well as the union set of all five lists. Genome build: Zv10r87 version of the zebrafish genome and transcriptome Supplementary files format and content: The processesd files are in Excel sheet format. The differential expression file include differential expression values Log2Fold change along with statistical significance. The rMATs file contain alternative splicing events analysis across wild type and fam50a KO mutants", "embryo head", null, "We extracted total RNA from embryo heads with Trizol ThermoFisher  according to manufacturer's instructions. N=20 embryos/pool. Samples were treated with DNase prior to RNAseq RNA seq libraries were prepared using the commercially available KAPA Stranded mRNA Seq Kit following the manufacturer\u2019s protocol. In brief  mRNA transcripts were first captured using magnetic oligo dT beads  fragmented using heat and magnesium  and reverse transcribed using random priming. During the 2nd strand synthesis  the cDNA:RNA hybrid was converted into double stranded cDNA dscDNA and dUTP incorporated into the 2nd cDNA strand. Illumina sequencing adapters were ligated to the dscDNA fragments and amplified to produce final RNA seq libraries. Libraries were indexed and pooled in an equimolar ratio prior to 50 bp single end sequencing on the same lane of a HiSeq 4000 Illumina. Sequence data were demultiplexed and Fastq files were generated using Bcl2Fastq conversion software Illumina.", "Embryos were obtained from natural matings of adult fam50a heterozygous KO mutants zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl  75 mg/L CaSO4  37.5 mg/L NaHC03  0.003% methylene blue at 28\u00b0C until 2 dpf.", "sample type:embryo head 2dpf|developmental stage:2 dpf type", "GSM4331445", "GSM4331445: KK S2; Danio rerio; RNA Seq", "GSM4331445", null, "1", "We extracted total RNA from embryo heads with Trizol ThermoFisher  according to manufacturer's instructions. N=20 embryos/pool. Samples were treated with DNase prior to RNAseq RNA seq libraries were prepared using the commercially available KAPA Stranded mRNA Seq Kit following the manufacturer's protocol. In brief  mRNA transcripts were first captured using magnetic oligo dT beads  fragmented using heat and magnesium  and reverse transcribed using random priming. During the 2nd strand synthesis  the cDNA:RNA hybrid was converted into double stranded cDNA dscDNA and dUTP incorporated into the 2nd cDNA strand. Illumina sequencing adapters were ligated to the dscDNA fragments and amplified to produce final RNA seq libraries. Libraries were indexed and pooled in an equimolar ratio prior to 50 bp single end sequencing on the same lane of a HiSeq 4000 Illumina. Sequence data were demultiplexed and Fastq files were generated using Bcl2Fastq conversion software Illumina.", "GEO Accession:GSM4331445", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP250312", null, null, "KK-S2_S2_L002_R1_001.fastq.gz", "fastq", 1717829328.0, 33682928.0, "GSM4331445 r2", "0:51 1:0", "A:428291698;C:421410178;G:396695686;T:471176777;N:254989", 51, 0, null, null, 428291698, 421410178, 396695686, 471176777, 254989, "SRX7777132", "SRS6196090", "SRA1045975", "GEO", "Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago", 1, 0.92887, null, 0.15607, null, 0.68887, null, 0.49171, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-02-21", "Hatching", "Embryo", "Head", "Nervous 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": ["56870"], "units": {}, "query_ms": 8.162876998540014}