run_metadata: 50692

This data as json

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
50692	SRR8244086	SRX5062208	SRS4078148	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep1	GSM3488834		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep1	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type 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°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488834	GSM3488834: ncapg2 gRNA3 rep1; Danio rerio; RNA Seq	GSM3488834		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488834	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S6_S6_L002_R1_001.fastq.gz	fastq	1199549988.0	23520588.0	GSM3488834 r2	0:51 1:0	A:291794226;C:299402070;G:278615395;T:329608144;N:130153	51	0			291794226	299402070	278615395	329608144	130153	SRX5062208	SRS4078148	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.93135		0.17445		0.66123		0.50823		51		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		United States	2018-11-26	Hatching	Embryo	Head	Nervous System