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
32806,SRR29478752,SRX24989905,SRS21691708,SRP515053,PRJNA1126173,Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity,GSE270309,Transcriptome Analysis,The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2,,pubmed:39289367,,head  scarb2a mut  rep 3,GSM8339369,,source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing,head  scarb2a mut  rep 3,done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.,head,,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut,GSM8339369,GSM8339369: head  scarb2a mut  rep 3; Danio rerio; RNA Seq,GSM8339369 r1,GSM8339369,1,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP515053,,,scarb2_mut3_R2.fastq.gz scarb2_mut3_R1.fastq.gz,fastq fastq,590803877.0,7118119.0,GSM8339369 r1,0:75 1:8,A:171152826;C:118382558;G:138973475;T:162287717;N:7301,75,8,,,171152826,118382558,138973475,162287717,7301,SRX24989905,SRS21691708,SRA1904886,"Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science","Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science",2,0.86187,0.0,0.06751,0.0,0.80081,1.0,0.47421,,75,8,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2024-06-20,Hatching,Embryo,Head,Nervous System
32807,SRR29478753,SRX24989904,SRS21691707,SRP515053,PRJNA1126173,Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity,GSE270309,Transcriptome Analysis,The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2,,pubmed:39289367,,head  scarb2a mut  rep 2,GSM8339368,,source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing,head  scarb2a mut  rep 2,done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.,head,,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut,GSM8339368,GSM8339368: head  scarb2a mut  rep 2; Danio rerio; RNA Seq,GSM8339368 r1,GSM8339368,1,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP515053,,,scarb2_mut2_R2.fastq.gz scarb2_mut2_R1.fastq.gz,fastq fastq,560228337.0,6749739.0,GSM8339368 r1,0:75 1:8,A:161395198;C:113034644;G:131199008;T:154592664;N:6823,75,8,,,161395198,113034644,131199008,154592664,6823,SRX24989904,SRS21691707,SRA1904886,"Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science","Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science",2,0.85633,0.0,0.06116,0.0,0.80438,1.0,0.47226,,75,8,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2024-06-20,Hatching,Embryo,Head,Nervous System
32808,SRR29478754,SRX24989903,SRS21691706,SRP515053,PRJNA1126173,Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity,GSE270309,Transcriptome Analysis,The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2,,pubmed:39289367,,head  scarb2a mut  rep 1,GSM8339367,,source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing,head  scarb2a mut  rep 1,done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.,head,,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut,GSM8339367,GSM8339367: head  scarb2a mut  rep 1; Danio rerio; RNA Seq,GSM8339367 r1,GSM8339367,1,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP515053,,,scarb2_mut1_R1.fastq.gz scarb2_mut1_R2.fastq.gz,fastq fastq,536045042.0,6458374.0,GSM8339367 r1,0:75 1:8,A:152863781;C:109210501;G:126922310;T:147041910;N:6540,75,8,,,152863781,109210501,126922310,147041910,6540,SRX24989903,SRS21691706,SRA1904886,"Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science","Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science",2,0.86464,0.0,0.06577,0.0,0.80359,1.0,0.48395,,75,8,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2024-06-20,Hatching,Embryo,Head,Nervous System
32809,SRR29478755,SRX24989902,SRS21691705,SRP515053,PRJNA1126173,Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity,GSE270309,Transcriptome Analysis,The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2,,pubmed:39289367,,head  wt  rep 4,GSM8339366,,source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing,head  wt  rep 4,done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.,head,,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,tissue:head|cell type:scarb2a+ cells|genotype:wt,GSM8339366,GSM8339366: head  wt  rep 4; Danio rerio; RNA Seq,GSM8339366 r1,GSM8339366,1,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP515053,,,scarb2_wt4_R1.fastq.gz scarb2_wt4_R2.fastq.gz,fastq fastq,723943430.0,8722210.0,GSM8339366 r1,0:75 1:8,A:206155698;C:145344454;G:172171717;T:200262536;N:9025,75,8,,,206155698,145344454,172171717,200262536,9025,SRX24989902,SRS21691705,SRA1904886,"Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science","Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science",2,0.86958,0.0,0.0737,0.0,0.79928,1.0,0.47906,,75,8,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2024-06-20,Hatching,Embryo,Head,Nervous System
32810,SRR29478756,SRX24989901,SRS21691704,SRP515053,PRJNA1126173,Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity,GSE270309,Transcriptome Analysis,The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2,,pubmed:39289367,,head  wt  rep 3,GSM8339365,,source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing,head  wt  rep 3,done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.,head,,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,tissue:head|cell type:scarb2a+ cells|genotype:wt,GSM8339365,GSM8339365: head  wt  rep 3; Danio rerio; RNA Seq,GSM8339365 r1,GSM8339365,1,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP515053,,,scarb2_wt3_R1.fastq.gz scarb2_wt3_R2.fastq.gz,fastq fastq,560881132.0,6757604.0,GSM8339365 r1,0:75 1:8,A:158992539;C:112696361;G:133852695;T:155332822;N:6715,75,8,,,158992539,112696361,133852695,155332822,6715,SRX24989901,SRS21691704,SRA1904886,"Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science","Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science",2,0.8706,0.0,0.07425,0.0,0.80038,1.0,0.47161,,75,8,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2024-06-20,Hatching,Embryo,Head,Nervous System
32811,SRR29478757,SRX24989900,SRS21691703,SRP515053,PRJNA1126173,Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity,GSE270309,Transcriptome Analysis,The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2,,pubmed:39289367,,head  wt  rep 1,GSM8339364,,source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing,head  wt  rep 1,done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.,head,,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,tissue:head|cell type:scarb2a+ cells|genotype:wt,GSM8339364,GSM8339364: head  wt  rep 1; Danio rerio; RNA Seq,GSM8339364 r1,GSM8339364,1,For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP515053,,,scarb2_wt1_R1.fastq.gz scarb2_wt1_R2.fastq.gz,fastq fastq,539653799.0,6501853.0,GSM8339364 r1,0:75 1:8,A:153571518;C:110489477;G:128477853;T:147108152;N:6799,75,8,,,153571518,110489477,128477853,147108152,6799,SRX24989900,SRS21691703,SRA1904886,"Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science","Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science",2,0.87359,0.0,0.07353,0.0,0.80184,1.0,0.47111,,75,8,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2024-06-20,Hatching,Embryo,Head,Nervous System
32863,SRR30114185,SRX25586802,SRS22237546,SRP523914,PRJNA1126282,Danio rerio Single cell Transcriptome,PRJNA1126282,Transcriptome Analysis,Single cell sequencing of Zebrafish model with RFC1 mutation for loss of function study. Samples from zebrafishes at 2 or 4 dpf isolated from the whole head or whole brain respectively. Libraries prepared and sequenced with 10X Genomics three prime Chromium kits.,,,,WT sc 2dpf,WT sc 2dpf S1 L003,,strain:Tgrfc1+/+|age:2dpf|collection date:2024 02 19|geo loc name:Canada: Montreal|sex:N/A|tissue:Head|genotype:Wild Type|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of danio rerio: 2dpf head,WT sc 2dpf,WT sc 2dpf,Four brains or three heads per condition from 4dpf or 2dpf larvae respectively were transferred into 1.5ml tubes containing 250 l of papain solution 100l papain  100l DNase I and 200l L cysteine per 5 mL of DMEM/F12. The tissue was digested 20min at 37C with pipetting every 10min. Enzymatic digestion was stopped with washing solution 65l glucose 45 %  50L HEPES 1M and 0.5ml FBS qsp 10ml DPBS 1X and centrifuged at 800g for 5min at 4C. Supernatant was removed and pellet was resuspended in 50l of washing solution. The cell suspension was filtered with a cell strainer to remove aggregates. Libraries were prepared with a three prime Chromium kit and sent for 10X Genomics sequencing at a depth of 250 million reads 100bp ea from Illumina NovaSeq6000.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP523914,,,WT_sc_2dpf_S1_L003_R2.fastq.gz WT_sc_2dpf_S1_L003_R1.fastq.gz,fastq fastq,56807165786.0,281223593.0,WT sc 2dpf S1 L003 R1.fastq.gz,0:101 1:101,A:15279867415;C:9333139424;G:10011041111;T:22182483036;N:634800,101,101,,,15279867415,9333139424,10011041111,22182483036,634800,SRX25586802,SRS22237546,SRA1936077,CHUM Research Center|Neurosciences,CHUM Research Center,2,0.07599,0.93395,0.0191,0.17781,0.97636,0.81215,0.61682,0.56234,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2024-08-02,Hatching,Embryo,Head,Nervous System
32864,SRR30114186,SRX25586801,SRS22237545,SRP523914,PRJNA1126282,Danio rerio Single cell Transcriptome,PRJNA1126282,Transcriptome Analysis,Single cell sequencing of Zebrafish model with RFC1 mutation for loss of function study. Samples from zebrafishes at 2 or 4 dpf isolated from the whole head or whole brain respectively. Libraries prepared and sequenced with 10X Genomics three prime Chromium kits.,,,,RFC1 KO sc 2dpf,RFC1 KO sc 2dpf S2 L003,,strain:Tgrfc1 / |age:2dpf|collection date:2024 02 19|geo loc name:Canada: Montreal|sex:N/A|tissue:Head|genotype:RFC1 KO|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of danio rerio: 2dpf head,RFC1 KO sc 2dpf,RFC1 KO sc 2dpf,Four brains or three heads per condition from 4dpf or 2dpf larvae respectively were transferred into 1.5ml tubes containing 250 l of papain solution 100l papain  100l DNase I and 200l L cysteine per 5 mL of DMEM/F12. The tissue was digested 20min at 37C with pipetting every 10min. Enzymatic digestion was stopped with washing solution 65l glucose 45 %  50L HEPES 1M and 0.5ml FBS qsp 10ml DPBS 1X and centrifuged at 800g for 5min at 4C. Supernatant was removed and pellet was resuspended in 50l of washing solution. The cell suspension was filtered with a cell strainer to remove aggregates. Libraries were prepared with a three prime Chromium kit and sent for 10X Genomics sequencing at a depth of 250 million reads 100bp ea from Illumina NovaSeq6000.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP523914,,,RFC1-KO_sc_2dpf_S2_L003_R1.fastq.gz RFC1-KO_sc_2dpf_S2_L003_R2.fastq.gz,fastq fastq,45448109280.0,224990640.0,RFC1 KO sc 2dpf S2 L003 R1.fastq.gz,0:101 1:101,A:12090767157;C:7635667126;G:8209912637;T:17511260653;N:501707,101,101,,,12090767157,7635667126,8209912637,17511260653,501707,SRX25586801,SRS22237545,SRA1936077,CHUM Research Center|Neurosciences,CHUM Research Center,2,0.09244,0.93268,0.02271,0.19887,0.97544,0.80955,0.6375,0.56143,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2024-08-02,Hatching,Embryo,Head,Nervous System
35385,SRR32649448,SRX27953870,SRS24319775,SRP569567,PRJNA1234533,Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb,GSE291626,Transcriptome Analysis,To understand how neural circuits are assembled  it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family  pcdh7b and pcdh11  are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus  but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast  two members of the delta2 protocadherin family  pcdh10b and pcdh17  are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus  while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36  48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.,,,,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,GSM8838717,,source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.,Olfactory Sensory Tissue,,10X Genomics V3.3,,tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP,GSM8838717,GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq,GSM8838717 r1,GSM8838717,1,10X Genomics V3.3,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP569567,,loader:fastq load.py,97364_S5_L001_I1_001.fastq.gz 97364_S5_L001_R1_001.fastq.gz 97364_S5_L001_R2_001.fastq.gz,fastq fastq fastq,7455743360.0,57351872.0,GSM8838717 r1,0:8 1:28 2:94,A:1588619193;C:1118423731;G:1232237797;T:1451670240;N:125007,8,28,94,,1588619193,1118423731,1232237797,1451670240,125007,SRX27953870,SRS24319775,SRA2091725,"Department of Neuroscience, University of Pennsylvania","Department of Neuroscience, University of Pennsylvania",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-11,Hatching,Embryo,Brain,Nervous System
35386,SRR32649449,SRX27953870,SRS24319775,SRP569567,PRJNA1234533,Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb,GSE291626,Transcriptome Analysis,To understand how neural circuits are assembled  it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family  pcdh7b and pcdh11  are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus  but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast  two members of the delta2 protocadherin family  pcdh10b and pcdh17  are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus  while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36  48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.,,,,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,GSM8838717,,source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.,Olfactory Sensory Tissue,,10X Genomics V3.3,,tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP,GSM8838717,GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq,GSM8838717 r1,GSM8838717,1,10X Genomics V3.3,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP569567,,loader:fastq load.py,97364_S5_L002_I1_001.fastq.gz 97364_S5_L002_R1_001.fastq.gz 97364_S5_L002_R2_001.fastq.gz,fastq fastq fastq,7445521460.0,57273242.0,GSM8838717 r2,0:8 1:28 2:94,A:1586585615;C:1115323543;G:1231863598;T:1449738354;N:173638,8,28,94,,1586585615,1115323543,1231863598,1449738354,173638,SRX27953870,SRS24319775,SRA2091725,"Department of Neuroscience, University of Pennsylvania","Department of Neuroscience, University of Pennsylvania",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-11,Hatching,Embryo,Brain,Nervous System
39828,SRR2437828,SRX1321832,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf normoxia,48hpf.normoxia.3.10329X16,48hpf.normoxia.3.10329X16,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X16_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,985942500.0,19718850.0,48hpf.normoxia.3.10329X16,0:50,A:251856100;C:223081125;G:216430606;T:294554748;N:19921,50,,,,251856100,223081125,216430606,294554748,19921,SRX1321832,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94791,,0.26704,,0.68708,,0.54445,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39830,SRR2433795,SRX1321830,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf Normoxia,60hpf.normoxia.3.,60hpf.normoxia.3.,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X8_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1112799950.0,22255999.0,60hpf.normoxia.3.,0:50,A:294304558;C:248234752;G:238088577;T:332109252;N:62811,50,,,,294304558,248234752,238088577,332109252,62811,SRX1321830,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94922,,0.34314,,0.67838,,0.51455,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39832,SRR2417497,SRX1321828,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf hypoxia,48hpf.hypoxia.3.10329X25,48hpf.hypoxia.3.10329X25,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X25_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1234710500.0,24694210.0,48hpf.hypoxia.3.10329X25,0:50,A:309392529;C:284311489;G:275471070;T:365515358;N:20054,50,,,,309392529,284311489,275471070,365515358,20054,SRX1321828,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94675,,0.25877,,0.71453,,0.5239,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-16,Hatching,Embryo,Brain,Nervous System
39833,SRR2417496,SRX1321827,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf Normoxia,60hpf.normoxia.2.10329X28,60hpf.normoxia.2.10329X28,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X28_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1015786750.0,20315735.0,60hpf.normoxia.2.10329X28,0:50,A:259102784;C:230364456;G:226008843;T:300294199;N:16468,50,,,,259102784,230364456,226008843,300294199,16468,SRX1321827,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95197,,0.30503,,0.68333,,0.52243,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-16,Hatching,Embryo,Brain,Nervous System
39837,SRR2342161,SRX1321823,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf hypoxia,60hpf.hypoxia.3.10329X27,60hpf.hypoxia.3.10329X27,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X27_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1073269500.0,21465390.0,60hpf.hypoxia.3.10329X27,0:50,A:280500644;C:237758835;G:234061287;T:320931292;N:17442,50,,,,280500644,237758835,234061287,320931292,17442,SRX1321823,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94774,,0.36354,,0.70065,,0.51075,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39838,SRR2341509,SRX1321822,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf normoxia,48hpf.normoxia.210329X26,48hpf.normoxia.210329X26,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X26_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1075868850.0,21517377.0,48hpf.normoxia.210329X26,0:50,A:271795722;C:246789566;G:240496674;T:316769688;N:17200,50,,,,271795722,246789566,240496674,316769688,17200,SRX1321822,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94644,,0.26805,,0.68745,,0.53833,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39844,SRR2241311,SRX1321816,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf Normoxia,60hpf.normoxia.1.10329X18,60hpf.normoxia.1.10329X18,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X18_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1118115050.0,22362301.0,60hpf.normoxia.1.10329X18,0:50,A:287072563;C:255244675;G:248573701;T:327203388;N:20723,50,,,,287072563,255244675,248573701,327203388,20723,SRX1321816,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.93238,,0.30064,,0.68574,,0.51934,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39845,SRR2240748,SRX1321815,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf hypoxia,60hpf.hypoxia.2.10329X17,60hpf.hypoxia.2.10329X17,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X17_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1074686900.0,21493738.0,60hpf.hypoxia.2.10329X17,0:50,A:276432361;C:244039609;G:234638386;T:319556004;N:20540,50,,,,276432361,244039609,234638386,319556004,20540,SRX1321815,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.9502,,0.3077,,0.6899,,0.50645,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-03,Hatching,Embryo,Brain,Nervous System
39846,SRR2239869,SRX1321814,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf hypoxia,48hpf.hypoxia.2.10329X15,48hpf.hypoxia.2.10329X15,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X15_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1111913550.0,22238271.0,48hpf.hypoxia.2.10329X15,0:50,A:288023952;C:248947169;G:243195362;T:331723738;N:23329,50,,,,288023952,248947169,243195362,331723738,23329,SRX1321814,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.93753,,0.34521,,0.70246,,0.51535,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39852,SRR2225888,SRX1321808,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf hypoxia,60hpf.hypoxia.1.10329X7,60hpf.hypoxia.1.10329X7,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X7_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1102232350.0,22044647.0,60hpf.hypoxia.1.10329X7,0:50,A:288570352;C:247978180;G:238128703;T:327492563;N:62552,50,,,,288570352,247978180,238128703,327492563,62552,SRX1321808,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94824,,0.31808,,0.69244,,0.51505,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39853,SRR2225789,SRX1321807,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf hypoxia,48hpf.hypoxia.1.10329X6,48hpf.hypoxia.1.10329X6,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X6_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1250042950.0,25000859.0,48hpf.hypoxia.1.10329X6,0:50,A:312511165;C:283310381;G:277279378;T:376891744;N:50282,50,,,,312511165,283310381,277279378,376891744,50282,SRX1321807,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94959,,0.28331,,0.68757,,0.53976,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Hatching,Embryo,Brain,Nervous System
39856,SRR2222835,SRX1321804,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf normoxia,48hpf.1.10329X1,48hpf.1.10329X1,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X1_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1215136450.0,24302729.0,48hpf.1.10329X1,0:50,A:291802893;C:276442849;G:277217342;T:369624915;N:48451,50,,,,291802893,276442849,277217342,369624915,48451,SRX1321804,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95575,,0.23021,,0.72679,,0.60296,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Hatching,Embryo,Brain,Nervous System
41297,SRR8173226,SRX4993779,SRS4029191,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,TRPC2 2,GSM2290761,,tissue:TRPC2 expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,TRPC2 2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,TRPC2 expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,GSM2290761,GSM2290761: TRPC2 2; Danio rerio; RNA Seq,GSM2290761,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290761,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0977_s_3_1_CTTGTA.fastq.gz FGC0977_s_3_2_CTTGTA.fastq.gz,fastq fastq,19333122000.0,96665610.0,GSM2290761 r1,0:100 1:100,A:5708354504;C:3932203444;G:3891575387;T:5798440967;N:2547698,100,100,,,5708354504,3932203444,3891575387,5798440967,2547698,SRX4993779,SRS4029191,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.89122,0.8929,0.18042,0.18083,0.7903,0.79182,0.61137,0.61123,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
41298,SRR8173225,SRX4993778,SRS4029190,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,TRPC2 1,GSM2290760,,tissue:TRPC2 expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,TRPC2 1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,TRPC2 expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,GSM2290760,GSM2290760: TRPC2 1; Danio rerio; RNA Seq,GSM2290760,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290760,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0977_s_3_1_GCCAAT.fastq.gz FGC0977_s_3_2_GCCAAT.fastq.gz,fastq fastq,19933298800.0,99666494.0,GSM2290760 r1,0:100 1:100,A:5663223656;C:4194804658;G:4197360143;T:5875323942;N:2586401,100,100,,,5663223656,4194804658,4197360143,5875323942,2586401,SRX4993778,SRS4029190,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.84844,0.84265,0.10791,0.1071,0.80886,0.81026,0.57202,0.57988,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
41299,SRR8173224,SRX4993777,SRS4029189,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,OMP 2,GSM2290759,,tissue:OMP expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,OMP 2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,OMP expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,GSM2290759,GSM2290759: OMP 2; Danio rerio; RNA Seq,GSM2290759,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290759,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0805_s_6_1_CTTGTA.fastq.gz FGC0805_s_6_2_CTTGTA.fastq.gz,fastq fastq,25768751000.0,128843755.0,GSM2290759 r1,0:100 1:100,A:6815152641;C:6065596177;G:5514207833;T:7360566579;N:13227770,100,100,,,6815152641,6065596177,5514207833,7360566579,13227770,SRX4993777,SRS4029189,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.94122,0.87325,0.12592,0.11103,0.7235,0.73563,0.4808,0.5167,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
41300,SRR8173223,SRX4993776,SRS4029188,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,OMP 1,GSM2290758,,tissue:OMP expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,OMP 1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,OMP expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,GSM2290758,GSM2290758: OMP 1; Danio rerio; RNA Seq,GSM2290758,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290758,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0805_s_6_2_GCCAAT.fastq.gz FGC0805_s_6_1_GCCAAT.fastq.gz,fastq fastq,24051320600.0,120256603.0,GSM2290758 r1,0:100 1:100,A:6601023193;C:5427909703;G:4902326306;T:7107644194;N:12417204,100,100,,,6601023193,5427909703,4902326306,7107644194,12417204,SRX4993776,SRS4029188,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.92859,0.84572,0.19924,0.173,0.71713,0.73154,0.54902,0.55157,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
48097,SRR7041789,SRX3973827,SRS3199286,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,gas6 /  mutant replicate 3 gas6mut,GSM3105075,,source name:dissected hindbrain|developmental stage:48 hpf /  mutant|tissue:hindbrain,gas6 /  mutant replicate 3 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf /  mutant|tissue:hindbrain,GSM3105075,GSM3105075: gas6 /  mutant replicate 3 gas6mut; Danio rerio; RNA Seq,GSM3105075,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105075,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,Mut3.fastq.gz,fastq,3795018900.0,37950189.0,GSM3105075 r1,0:100,A:918996199;C:928143353;G:923182529;T:1021402181;N:3294638,100,,,,918996199,928143353,923182529,1021402181,3294638,SRX3973827,SRS3199286,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.95946,,0.06073,,0.68235,,0.46562,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48098,SRR7041788,SRX3973826,SRS3199287,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,gas6 /  mutant replicate 2 gas6mut,GSM3105074,,source name:dissected hindbrain|developmental stage:48 hpf /  mutant|tissue:hindbrain,gas6 /  mutant replicate 2 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf /  mutant|tissue:hindbrain,GSM3105074,GSM3105074: gas6 /  mutant replicate 2 gas6mut; Danio rerio; RNA Seq,GSM3105074,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105074,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,Mut2.fastq.gz,fastq,3729663500.0,37296635.0,GSM3105074 r1,0:100,A:909818849;C:902636895;G:904978335;T:1008966488;N:3262933,100,,,,909818849,902636895,904978335,1008966488,3262933,SRX3973826,SRS3199287,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.95717,,0.06681,,0.68217,,0.46864,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48099,SRR7041787,SRX3973825,SRS3199285,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,gas6 /  mutant replicate 1 gas6mut,GSM3105073,,source name:dissected hindbrain|developmental stage:48 hpf /  mutant|tissue:hindbrain,gas6 /  mutant replicate 1 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf /  mutant|tissue:hindbrain,GSM3105073,GSM3105073: gas6 /  mutant replicate 1 gas6mut; Danio rerio; RNA Seq,GSM3105073,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105073,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,Mut1.fastq.gz,fastq,2554222700.0,25542227.0,GSM3105073 r1,0:100,A:629483819;C:619623433;G:604226674;T:698705739;N:2183035,100,,,,629483819,619623433,604226674,698705739,2183035,SRX3973825,SRS3199285,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.9561,,0.07094,,0.67838,,0.46772,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48100,SRR7041786,SRX3973824,SRS3199283,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,wildtype control replicate 3 gas6mut,GSM3105072,,source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain,wildtype control replicate 3 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf control|tissue:hindbrain,GSM3105072,GSM3105072: wildtype control replicate 3 gas6mut; Danio rerio; RNA Seq,GSM3105072,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105072,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,WT3.fastq.gz,fastq,3024416800.0,30244168.0,GSM3105072 r1,0:100,A:748173237;C:725813083;G:722763689;T:825021244;N:2645547,100,,,,748173237,725813083,722763689,825021244,2645547,SRX3973824,SRS3199283,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.95777,,0.0748,,0.69059,,0.46902,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48101,SRR7041785,SRX3973823,SRS3199284,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,wildtype control replicate 2 gas6mut,GSM3105071,,source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain,wildtype control replicate 2 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf control|tissue:hindbrain,GSM3105071,GSM3105071: wildtype control replicate 2 gas6mut; Danio rerio; RNA Seq,GSM3105071,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105071,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,WT2.fastq.gz,fastq,3358506900.0,33585069.0,GSM3105071 r1,0:100,A:816072735;C:817548352;G:813692655;T:908273519;N:2919639,100,,,,816072735,817548352,813692655,908273519,2919639,SRX3973823,SRS3199284,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.9596,,0.06574,,0.69197,,0.46749,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48102,SRR7041784,SRX3973822,SRS3199282,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,wildtype control replicate 1 gas6mut,GSM3105070,,source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain,wildtype control replicate 1 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf control|tissue:hindbrain,GSM3105070,GSM3105070: wildtype control replicate 1 gas6mut; Danio rerio; RNA Seq,GSM3105070,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105070,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,WT1.fastq.gz,fastq,3390648900.0,33906489.0,GSM3105070 r1,0:100,A:815584808;C:833592815;G:824903141;T:913622836;N:2945300,100,,,,815584808,833592815,824903141,913622836,2945300,SRX3973822,SRS3199282,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.96267,,0.05448,,0.69798,,0.46774,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
50664,SRR8244112,SRX5062217,SRS4078157,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 Cas9 rep5,GSM3488843,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep5,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,GSM3488843,GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq,GSM3488843,,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:GSM3488843,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S15_S15_L001_R1_001.fastq.gz,fastq,1104353541.0,21653991.0,GSM3488843 r1,0:51 1:0,A:271859663;C:271742909;G:255256859;T:305383003;N:111107,51,0,,,271859663,271742909,255256859,305383003,111107,SRX5062217,SRS4078157,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92793,,0.15706,,0.6686,,0.48785,,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
50665,SRR8244113,SRX5062217,SRS4078157,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 Cas9 rep5,GSM3488843,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep5,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,GSM3488843,GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq,GSM3488843,,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:GSM3488843,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S15_S15_L002_R1_001.fastq.gz,fastq,1107061335.0,21707085.0,GSM3488843 r2,0:51 1:0,A:272582305;C:272363181;G:255837702;T:306158767;N:119380,51,0,,,272582305,272363181,255837702,306158767,119380,SRX5062217,SRS4078157,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.9291,,0.15688,,0.66939,,0.4874,,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
50666,SRR8244114,SRX5062217,SRS4078157,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 Cas9 rep5,GSM3488843,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep5,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,GSM3488843,GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq,GSM3488843,,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:GSM3488843,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S15_S15_L003_R1_001.fastq.gz,fastq,1108045737.0,21726387.0,GSM3488843 r3,0:51 1:0,A:272751963;C:272598901;G:256278919;T:306301107;N:114847,51,0,,,272751963,272598901,256278919,306301107,114847,SRX5062217,SRS4078157,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92569,,0.15636,,0.67107,,0.48848,,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
50667,SRR8244109,SRX5062216,SRS4078156,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 Cas9 rep4,GSM3488842,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep4,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,GSM3488842,GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq,GSM3488842,,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:GSM3488842,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S14_S14_L001_R1_001.fastq.gz,fastq,1006920234.0,19743534.0,GSM3488842 r1,0:51 1:0,A:250914585;C:242617209;G:230819870;T:282467195;N:101375,51,0,,,250914585,242617209,230819870,282467195,101375,SRX5062216,SRS4078156,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92511,,0.14656,,0.66255,,0.4737,,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
50668,SRR8244110,SRX5062216,SRS4078156,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 Cas9 rep4,GSM3488842,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep4,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,GSM3488842,GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq,GSM3488842,,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:GSM3488842,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S14_S14_L002_R1_001.fastq.gz,fastq,1011359019.0,19830569.0,GSM3488842 r2,0:51 1:0,A:252043979;C:243615191;G:231854021;T:283736741;N:109087,51,0,,,252043979,243615191,231854021,283736741,109087,SRX5062216,SRS4078156,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92626,,0.14636,,0.66113,,0.47444,,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
50669,SRR8244111,SRX5062216,SRS4078156,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 Cas9 rep4,GSM3488842,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep4,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,GSM3488842,GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq,GSM3488842,,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:GSM3488842,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S14_S14_L003_R1_001.fastq.gz,fastq,1013403201.0,19870651.0,GSM3488842 r3,0:51 1:0,A:252575184;C:244090867;G:232476280;T:284156056;N:104814,51,0,,,252575184,244090867,232476280,284156056,104814,SRX5062216,SRS4078156,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92435,,0.14732,,0.66178,,0.47364,,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
50670,SRR8244106,SRX5062215,SRS4078155,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 Cas9 rep3,GSM3488841,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep3,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,GSM3488841,GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq,GSM3488841,,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:GSM3488841,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S13_S13_L001_R1_001.fastq.gz,fastq,994771983.0,19505333.0,GSM3488841 r1,0:51 1:0,A:242678169;C:243280763;G:232480047;T:276234852;N:98152,51,0,,,242678169,243280763,232480047,276234852,98152,SRX5062215,SRS4078155,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.93015,,0.13516,,0.66338,,0.47268,,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
50671,SRR8244107,SRX5062215,SRS4078155,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 Cas9 rep3,GSM3488841,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep3,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,GSM3488841,GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq,GSM3488841,,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:GSM3488841,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S13_S13_L002_R1_001.fastq.gz,fastq,1000961139.0,19626689.0,GSM3488841 r2,0:51 1:0,A:244193037;C:244754957;G:233915568;T:277991308;N:106269,51,0,,,244193037,244754957,233915568,277991308,106269,SRX5062215,SRS4078155,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92992,,0.13363,,0.66143,,0.47596,,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
50672,SRR8244108,SRX5062215,SRS4078155,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 Cas9 rep3,GSM3488841,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep3,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,GSM3488841,GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq,GSM3488841,,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:GSM3488841,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S13_S13_L003_R1_001.fastq.gz,fastq,1002999507.0,19666657.0,GSM3488841 r3,0:51 1:0,A:244687169;C:245305809;G:234523016;T:278381509;N:102004,51,0,,,244687169,245305809,234523016,278381509,102004,SRX5062215,SRS4078155,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92775,,0.13351,,0.66143,,0.46661,,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
50673,SRR8244103,SRX5062214,SRS4078154,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 Cas9 rep2,GSM3488840,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep2,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,GSM3488840,GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq,GSM3488840,,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:GSM3488840,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S12_S12_L001_R1_001.fastq.gz,fastq,1228909821.0,24096271.0,GSM3488840 r1,0:51 1:0,A:298212594;C:304802527;G:286549620;T:339221142;N:123938,51,0,,,298212594,304802527,286549620,339221142,123938,SRX5062214,SRS4078154,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92713,,0.14665,,0.66547,,0.49543,,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
50674,SRR8244104,SRX5062214,SRS4078154,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 Cas9 rep2,GSM3488840,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep2,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,GSM3488840,GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq,GSM3488840,,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:GSM3488840,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S12_S12_L002_R1_001.fastq.gz,fastq,1235947821.0,24234271.0,GSM3488840 r2,0:51 1:0,A:299963399;C:306522449;G:288138725;T:341187728;N:135520,51,0,,,299963399,306522449,288138725,341187728,135520,SRX5062214,SRS4078154,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92688,,0.14676,,0.66669,,0.49493,,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
50675,SRR8244105,SRX5062214,SRS4078154,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 Cas9 rep2,GSM3488840,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 rep2,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,GSM3488840,GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq,GSM3488840,,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:GSM3488840,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S12_S12_L003_R1_001.fastq.gz,fastq,1236009531.0,24235481.0,GSM3488840 r3,0:51 1:0,A:300016555;C:306493432;G:288334228;T:341035993;N:129323,51,0,,,300016555,306493432,288334228,341035993,129323,SRX5062214,SRS4078154,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92486,,0.1456,,0.66576,,0.49558,,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
50676,SRR8244100,SRX5062213,SRS4078153,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 Cas9 rep1,GSM3488839,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 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,GSM3488839,GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq,GSM3488839,,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:GSM3488839,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S11_S11_L001_R1_001.fastq.gz,fastq,1090927536.0,21390736.0,GSM3488839 r1,0:51 1:0,A:271017299;C:263543757;G:249256774;T:306999426;N:110280,51,0,,,271017299,263543757,249256774,306999426,110280,SRX5062213,SRS4078153,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92359,,0.15259,,0.65662,,0.47976,,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
50677,SRR8244101,SRX5062213,SRS4078153,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 Cas9 rep1,GSM3488839,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 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,GSM3488839,GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq,GSM3488839,,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:GSM3488839,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S11_S11_L002_R1_001.fastq.gz,fastq,1096424775.0,21498525.0,GSM3488839 r2,0:51 1:0,A:272497776;C:264812949;G:250461572;T:308534070;N:118408,51,0,,,272497776,264812949,250461572,308534070,118408,SRX5062213,SRS4078153,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92537,,0.15294,,0.6564,,0.48091,,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
50678,SRR8244102,SRX5062213,SRS4078153,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 Cas9 rep1,GSM3488839,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 Cas9 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,GSM3488839,GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq,GSM3488839,,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:GSM3488839,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S11_S11_L003_R1_001.fastq.gz,fastq,1097236746.0,21514446.0,GSM3488839 r3,0:51 1:0,A:272640711;C:265014569;G:250849083;T:308618948;N:113435,51,0,,,272640711,265014569,250849083,308618948,113435,SRX5062213,SRS4078153,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92126,,0.15288,,0.65758,,0.48139,,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
50679,SRR8244097,SRX5062212,SRS4078152,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 rep5,GSM3488838,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep5,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,GSM3488838,GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq,GSM3488838,,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:GSM3488838,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S10_S10_L001_R1_001.fastq.gz,fastq,1108278552.0,21730952.0,GSM3488838 r1,0:51 1:0,A:275932434;C:266759397;G:253066873;T:312409285;N:110563,51,0,,,275932434,266759397,253066873,312409285,110563,SRX5062212,SRS4078152,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92384,,0.15395,,0.65981,,0.47171,,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
50680,SRR8244098,SRX5062212,SRS4078152,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 rep5,GSM3488838,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep5,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,GSM3488838,GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq,GSM3488838,,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:GSM3488838,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S10_S10_L002_R1_001.fastq.gz,fastq,1112805975.0,21819725.0,GSM3488838 r2,0:51 1:0,A:277089394;C:267821306;G:254016353;T:313757990;N:120932,51,0,,,277089394,267821306,254016353,313757990,120932,SRX5062212,SRS4078152,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92569,,0.15411,,0.66042,,0.47795,,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
50681,SRR8244099,SRX5062212,SRS4078152,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 rep5,GSM3488838,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep5,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,GSM3488838,GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq,GSM3488838,,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:GSM3488838,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S10_S10_L003_R1_001.fastq.gz,fastq,1113574698.0,21834798.0,GSM3488838 r3,0:51 1:0,A:277244311;C:268029085;G:254374324;T:313812352;N:114626,51,0,,,277244311,268029085,254374324,313812352,114626,SRX5062212,SRS4078152,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92312,,0.15403,,0.66131,,0.475,,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
50682,SRR8244094,SRX5062211,SRS4078151,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 rep4,GSM3488837,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep4,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,GSM3488837,GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq,GSM3488837,,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:GSM3488837,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S9_S9_L001_R1_001.fastq.gz,fastq,989308914.0,19398214.0,GSM3488837 r1,0:51 1:0,A:244142324;C:238841091;G:227525215;T:278701440;N:98844,51,0,,,244142324,238841091,227525215,278701440,98844,SRX5062211,SRS4078151,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92369,,0.14203,,0.66107,,0.47606,,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
50683,SRR8244095,SRX5062211,SRS4078151,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 rep4,GSM3488837,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep4,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,GSM3488837,GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq,GSM3488837,,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:GSM3488837,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S9_S9_L002_R1_001.fastq.gz,fastq,995567991.0,19520941.0,GSM3488837 r2,0:51 1:0,A:245733399;C:240305756;G:228973873;T:280447377;N:107586,51,0,,,245733399,240305756,228973873,280447377,107586,SRX5062211,SRS4078151,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.9253,,0.14267,,0.66156,,0.47641,,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
50684,SRR8244096,SRX5062211,SRS4078151,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 rep4,GSM3488837,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep4,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,GSM3488837,GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq,GSM3488837,,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:GSM3488837,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S9_S9_L003_R1_001.fastq.gz,fastq,995686107.0,19523257.0,GSM3488837 r3,0:51 1:0,A:245728339;C:240375764;G:229145692;T:280334702;N:101610,51,0,,,245728339,240375764,229145692,280334702,101610,SRX5062211,SRS4078151,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.9222,,0.1414,,0.66129,,0.47546,,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
50685,SRR8244091,SRX5062210,SRS4078150,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 rep3,GSM3488836,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep3,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,GSM3488836,GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq,GSM3488836,,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:GSM3488836,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S8_S8_L001_R1_001.fastq.gz,fastq,1240305720.0,24319720.0,GSM3488836 r1,0:51 1:0,A:306283941;C:302350915;G:285978262;T:345570234;N:122368,51,0,,,306283941,302350915,285978262,345570234,122368,SRX5062210,SRS4078150,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92431,,0.15332,,0.6664,,0.48826,,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
50686,SRR8244092,SRX5062210,SRS4078150,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 rep3,GSM3488836,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep3,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,GSM3488836,GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq,GSM3488836,,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:GSM3488836,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S8_S8_L002_R1_001.fastq.gz,fastq,1244343033.0,24398883.0,GSM3488836 r2,0:51 1:0,A:307334069;C:303294657;G:286891055;T:346690285;N:132967,51,0,,,307334069,303294657,286891055,346690285,132967,SRX5062210,SRS4078150,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92593,,0.15367,,0.66604,,0.4866,,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
50687,SRR8244093,SRX5062210,SRS4078150,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 rep3,GSM3488836,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep3,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,GSM3488836,GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq,GSM3488836,,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:GSM3488836,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S8_S8_L003_R1_001.fastq.gz,fastq,1246263744.0,24436544.0,GSM3488836 r3,0:51 1:0,A:307763481;C:303768183;G:287566818;T:347039016;N:126246,51,0,,,307763481,303768183,287566818,347039016,126246,SRX5062210,SRS4078150,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92279,,0.15465,,0.6662,,0.48909,,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
50688,SRR8244088,SRX5062209,SRS4078149,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 rep2,GSM3488835,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep2,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,GSM3488835,GSM3488835: ncapg2 gRNA3 rep2; Danio rerio; RNA Seq,GSM3488835,,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:GSM3488835,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S7_S7_L001_R1_001.fastq.gz,fastq,1047071514.0,20530814.0,GSM3488835 r1,0:51 1:0,A:256902869;C:258344237;G:242502701;T:289217725;N:103982,51,0,,,256902869,258344237,242502701,289217725,103982,SRX5062209,SRS4078149,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92959,,0.1635,,0.66647,,0.49696,,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
50689,SRR8244089,SRX5062209,SRS4078149,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 rep2,GSM3488835,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep2,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,GSM3488835,GSM3488835: ncapg2 gRNA3 rep2; Danio rerio; RNA Seq,GSM3488835,,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:GSM3488835,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S7_S7_L002_R1_001.fastq.gz,fastq,1051491480.0,20617480.0,GSM3488835 r2,0:51 1:0,A:257964459;C:259432490;G:243475655;T:290506674;N:112202,51,0,,,257964459,259432490,243475655,290506674,112202,SRX5062209,SRS4078149,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.93114,,0.16334,,0.66849,,0.49762,,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
50690,SRR8244090,SRX5062209,SRS4078149,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 rep2,GSM3488835,,source name:embryo head|tissue:embryo head|time point:2 dpf,ncapg2 gRNA3 rep2,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,GSM3488835,GSM3488835: ncapg2 gRNA3 rep2; Danio rerio; RNA Seq,GSM3488835,,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:GSM3488835,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S7_S7_L003_R1_001.fastq.gz,fastq,1052688603.0,20640953.0,GSM3488835 r3,0:51 1:0,A:258264531;C:259707847;G:243893492;T:290716219;N:106514,51,0,,,258264531,259707847,243893492,290716219,106514,SRX5062209,SRS4078149,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92874,,0.16404,,0.666,,0.50389,,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
50691,SRR8244085,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_L001_R1_001.fastq.gz,fastq,1191686247.0,23366397.0,GSM3488834 r1,0:51 1:0,A:289846111;C:297515045;G:276860101;T:327344773;N:120217,51,0,,,289846111,297515045,276860101,327344773,120217,SRX5062208,SRS4078148,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92975,,0.17522,,0.66302,,0.50487,,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
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
50693,SRR8244087,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_L003_R1_001.fastq.gz,fastq,1198298652.0,23496052.0,GSM3488834 r3,0:51 1:0,A:291514396;C:299035235;G:278501070;T:329123391;N:124560,51,0,,,291514396,299035235,278501070,329123391,124560,SRX5062208,SRS4078148,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92761,,0.17518,,0.66332,,0.5075,,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
50694,SRR8244082,SRX5062207,SRS4078147,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,,phenol red rep5,GSM3488833,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep5,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 red,GSM3488833,GSM3488833: phenol red rep5; Danio rerio; RNA Seq,GSM3488833,,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:GSM3488833,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S5_S5_L001_R1_001.fastq.gz,fastq,1159968327.0,22744477.0,GSM3488833 r1,0:51 1:0,A:286238785;C:282775459;G:266662113;T:324177455;N:114515,51,0,,,286238785,282775459,266662113,324177455,114515,SRX5062207,SRS4078147,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92591,,0.15107,,0.66511,,0.48651,,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
50695,SRR8244083,SRX5062207,SRS4078147,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,,phenol red rep5,GSM3488833,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep5,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 red,GSM3488833,GSM3488833: phenol red rep5; Danio rerio; RNA Seq,GSM3488833,,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:GSM3488833,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S5_S5_L002_R1_001.fastq.gz,fastq,1167988485.0,22901735.0,GSM3488833 r2,0:51 1:0,A:288194571;C:284729076;G:268455130;T:326485683;N:124025,51,0,,,288194571,284729076,268455130,326485683,124025,SRX5062207,SRS4078147,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92677,,0.15299,,0.66486,,0.48959,,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
50696,SRR8244084,SRX5062207,SRS4078147,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,,phenol red rep5,GSM3488833,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep5,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 red,GSM3488833,GSM3488833: phenol red rep5; Danio rerio; RNA Seq,GSM3488833,,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:GSM3488833,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S5_S5_L003_R1_001.fastq.gz,fastq,1169477175.0,22930925.0,GSM3488833 r3,0:51 1:0,A:288662075;C:285050661;G:268977814;T:326667234;N:119391,51,0,,,288662075,285050661,268977814,326667234,119391,SRX5062207,SRS4078147,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92353,,0.15263,,0.66371,,0.48436,,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
50697,SRR8244079,SRX5062206,SRS4078146,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,,phenol red rep4,GSM3488832,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep4,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 red,GSM3488832,GSM3488832: phenol red rep4; Danio rerio; RNA Seq,GSM3488832,,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:GSM3488832,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S4_S4_L001_R1_001.fastq.gz,fastq,922605606.0,18090306.0,GSM3488832 r1,0:51 1:0,A:224888320;C:228719312;G:214749825;T:254159559;N:88590,51,0,,,224888320,228719312,214749825,254159559,88590,SRX5062206,SRS4078146,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92938,,0.16094,,0.66949,,0.49837,,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
50698,SRR8244080,SRX5062206,SRS4078146,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,,phenol red rep4,GSM3488832,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep4,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 red,GSM3488832,GSM3488832: phenol red rep4; Danio rerio; RNA Seq,GSM3488832,,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:GSM3488832,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S4_S4_L002_R1_001.fastq.gz,fastq,927811737.0,18192387.0,GSM3488832 r2,0:51 1:0,A:226207683;C:229941498;G:215897068;T:255669930;N:95558,51,0,,,226207683,229941498,215897068,255669930,95558,SRX5062206,SRS4078146,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.9298,,0.16225,,0.66977,,0.49705,,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
50699,SRR8244081,SRX5062206,SRS4078146,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,,phenol red rep4,GSM3488832,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep4,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 red,GSM3488832,GSM3488832: phenol red rep4; Danio rerio; RNA Seq,GSM3488832,,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:GSM3488832,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S4_S4_L003_R1_001.fastq.gz,fastq,929928747.0,18233897.0,GSM3488832 r3,0:51 1:0,A:226705927;C:230492844;G:216518196;T:256121312;N:90468,51,0,,,226705927,230492844,216518196,256121312,90468,SRX5062206,SRS4078146,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92696,,0.1594,,0.66906,,0.49888,,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
50700,SRR8244076,SRX5062205,SRS4078145,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,,phenol red rep3,GSM3488831,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep3,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 red,GSM3488831,GSM3488831: phenol red rep3; Danio rerio; RNA Seq,GSM3488831,,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:GSM3488831,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S3_S3_L001_R1_001.fastq.gz,fastq,897162063.0,17591413.0,GSM3488831 r1,0:51 1:0,A:221202889;C:218769075;G:206704109;T:250396873;N:89117,51,0,,,221202889,218769075,206704109,250396873,89117,SRX5062205,SRS4078145,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92557,,0.151,,0.6618,,0.48267,,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
50701,SRR8244077,SRX5062205,SRS4078145,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,,phenol red rep3,GSM3488831,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep3,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 red,GSM3488831,GSM3488831: phenol red rep3; Danio rerio; RNA Seq,GSM3488831,,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:GSM3488831,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S3_S3_L002_R1_001.fastq.gz,fastq,900077070.0,17648570.0,GSM3488831 r2,0:51 1:0,A:221806455;C:219590198;G:207296255;T:251287886;N:96276,51,0,,,221806455,219590198,207296255,251287886,96276,SRX5062205,SRS4078145,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92893,,0.15176,,0.6648,,0.48203,,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
50702,SRR8244078,SRX5062205,SRS4078145,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,,phenol red rep3,GSM3488831,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep3,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 red,GSM3488831,GSM3488831: phenol red rep3; Danio rerio; RNA Seq,GSM3488831,,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:GSM3488831,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S3_S3_L003_R1_001.fastq.gz,fastq,902126709.0,17688759.0,GSM3488831 r3,0:51 1:0,A:222335986;C:220068562;G:207953397;T:251675877;N:92887,51,0,,,222335986,220068562,207953397,251675877,92887,SRX5062205,SRS4078145,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92511,,0.15132,,0.66332,,0.48892,,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
50703,SRR8244073,SRX5062204,SRS4078143,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,,phenol red rep2,GSM3488830,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep2,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 red,GSM3488830,GSM3488830: phenol red rep2; Danio rerio; RNA Seq,GSM3488830,,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:GSM3488830,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S2_S2_L001_R1_001.fastq.gz,fastq,883107330.0,17315830.0,GSM3488830 r1,0:51 1:0,A:217899984;C:213724390;G:202494755;T:248901144;N:87057,51,0,,,217899984,213724390,202494755,248901144,87057,SRX5062204,SRS4078143,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.9212,,0.13988,,0.65951,,0.47797,,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
50704,SRR8244074,SRX5062204,SRS4078143,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,,phenol red rep2,GSM3488830,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep2,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 red,GSM3488830,GSM3488830: phenol red rep2; Danio rerio; RNA Seq,GSM3488830,,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:GSM3488830,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S2_S2_L002_R1_001.fastq.gz,fastq,888404190.0,17419690.0,GSM3488830 r2,0:51 1:0,A:219288459;C:214987628;G:203666399;T:250368228;N:93476,51,0,,,219288459,214987628,203666399,250368228,93476,SRX5062204,SRS4078143,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92249,,0.14008,,0.65833,,0.46889,,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
50705,SRR8244075,SRX5062204,SRS4078143,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,,phenol red rep2,GSM3488830,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red rep2,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 red,GSM3488830,GSM3488830: phenol red rep2; Danio rerio; RNA Seq,GSM3488830,,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:GSM3488830,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S2_S2_L003_R1_001.fastq.gz,fastq,890160681.0,17454131.0,GSM3488830 r3,0:51 1:0,A:219700893;C:215424116;G:204218333;T:250727670;N:89669,51,0,,,219700893,215424116,204218333,250727670,89669,SRX5062204,SRS4078143,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92091,,0.13895,,0.65977,,0.47244,,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
50706,SRR8244070,SRX5062203,SRS4078144,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,,phenol red rep1,GSM3488829,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red 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 red,GSM3488829,GSM3488829: phenol red rep1; Danio rerio; RNA Seq,GSM3488829,,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:GSM3488829,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S1_S1_L001_R1_001.fastq.gz,fastq,873733071.0,17132021.0,GSM3488829 r1,0:51 1:0,A:217088547;C:211224249;G:199952646;T:245380769;N:86860,51,0,,,217088547,211224249,199952646,245380769,86860,SRX5062203,SRS4078144,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.924,,0.15017,,0.6495,,0.47585,,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
50707,SRR8244071,SRX5062203,SRS4078144,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,,phenol red rep1,GSM3488829,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red 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 red,GSM3488829,GSM3488829: phenol red rep1; Danio rerio; RNA Seq,GSM3488829,,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:GSM3488829,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S1_S1_L002_R1_001.fastq.gz,fastq,877719078.0,17210178.0,GSM3488829 r2,0:51 1:0,A:218155528;C:212129394;G:200837990;T:246501710;N:94456,51,0,,,218155528,212129394,200837990,246501710,94456,SRX5062203,SRS4078144,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92461,,0.14859,,0.6491,,0.47655,,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
50708,SRR8244072,SRX5062203,SRS4078144,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,,phenol red rep1,GSM3488829,,source name:embryo head|tissue:embryo head|time point:2 dpf red,phenol red 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 red,GSM3488829,GSM3488829: phenol red rep1; Danio rerio; RNA Seq,GSM3488829,,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:GSM3488829,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP170713,,,4948-S1_S1_L003_R1_001.fastq.gz,fastq,879501273.0,17245123.0,GSM3488829 r3,0:51 1:0,A:218561820;C:212596855;G:201358917;T:246893407;N:90274,51,0,,,218561820,212596855,201358917,246893407,90274,SRX5062203,SRS4078144,SRA814826,GEO,"Center for Human Disease Modeling, Duke University Medical Center",1,0.92318,,0.14661,,0.6491,,0.47527,,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
56512,SRR10988549,SRX7649999,SRS6079496,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib3,GSM4289907,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib3,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289907,GSM4289907: head  2d rw440 sib3; Danio rerio; RNA Seq,GSM4289907,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289907,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib3_R2.fastq.gz 2d_rw440_sib3_R1.fastq.gz,fastq fastq,3140682329.0,10457484.0,GSM4289907 r1,0:150.21 1:150.12,A:760684292;C:777389008;G:783922642;T:818121129;N:565258,150,150,,,760684292,777389008,783922642,818121129,565258,SRX7649999,SRS6079496,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93527,0.95251,0.03293,0.02826,0.72032,0.73669,0.4787,0.47899,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56513,SRR10988548,SRX7649998,SRS6079495,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib2,GSM4289906,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib2,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289906,GSM4289906: head  2d rw440 sib2; Danio rerio; RNA Seq,GSM4289906,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289906,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib2_R1.fastq.gz 2d_rw440_sib2_R2.fastq.gz,fastq fastq,3194598681.0,10634398.0,GSM4289906 r1,0:150.24 1:150.17,A:771547062;C:789590364;G:796831526;T:835985747;N:643982,150,150,,,771547062,789590364,796831526,835985747,643982,SRX7649998,SRS6079495,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93377,0.95416,0.02628,0.02182,0.72989,0.74805,0.46631,0.47654,149,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56514,SRR10988547,SRX7649997,SRS6079494,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib1,GSM4289905,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib1,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289905,GSM4289905: head  2d rw440 sib1; Danio rerio; RNA Seq,GSM4289905,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289905,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib1_R1.fastq.gz 2d_rw440_sib1_R2.fastq.gz,fastq fastq,2654979688.0,8840507.0,GSM4289905 r1,0:150.19 1:150.13,A:624000299;C:675145222;G:678635011;T:676731946;N:467210,150,150,,,624000299,675145222,678635011,676731946,467210,SRX7649997,SRS6079494,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.9317,0.94861,0.06364,0.05753,0.72811,0.75055,0.50771,0.52256,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56515,SRR10988546,SRX7649996,SRS6079493,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut3,GSM4289904,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut3,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289904,GSM4289904: head  2d rw440 mut3; Danio rerio; RNA Seq,GSM4289904,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289904,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut3_R1.fastq.gz 2d_rw440_mut3_R2.fastq.gz,fastq fastq,3282506507.0,10958106.0,GSM4289904 r1,0:149.81 1:149.74,A:781014809;C:816143245;G:824711112;T:858035111;N:2602230,149,149,,,781014809,816143245,824711112,858035111,2602230,SRX7649996,SRS6079493,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93293,0.95901,0.02641,0.023,0.74408,0.76449,0.48032,0.475,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56516,SRR10988545,SRX7649995,SRS6079492,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut2,GSM4289903,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut2,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289903,GSM4289903: head  2d rw440 mut2; Danio rerio; RNA Seq,GSM4289903,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289903,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut2_R2.fastq.gz 2d_rw440_mut2_R1.fastq.gz,fastq fastq,2673347852.0,8908620.0,GSM4289903 r1,0:150.07 1:150.01,A:641733072;C:667262119;G:672992510;T:690242042;N:1118109,150,150,,,641733072,667262119,672992510,690242042,1118109,SRX7649995,SRS6079492,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93754,0.95755,0.03962,0.0352,0.72234,0.73963,0.47668,0.49072,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56517,SRR10988544,SRX7649994,SRS6079491,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut1,GSM4289902,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut1,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289902,GSM4289902: head  2d rw440 mut1; Danio rerio; RNA Seq,GSM4289902,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289902,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut1_R1.fastq.gz 2d_rw440_mut1_R2.fastq.gz,fastq fastq,2609801785.0,8695280.0,GSM4289902 r1,0:150.10 1:150.04,A:629026157;C:649393814;G:654616712;T:676204104;N:560998,150,150,,,629026157,649393814,654616712,676204104,560998,SRX7649994,SRS6079491,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93478,0.95296,0.02959,0.0259,0.72458,0.74209,0.4765,0.47804,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56853,SRR11140724,SRX7777140,SRS6196095,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,,pubmed:32703943,,KK S10,GSM4331453,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S10,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331453,GSM4331453: KK S10; Danio rerio; RNA Seq,GSM4331453,,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:GSM4331453,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S10_S10_L001_R1_001.fastq.gz,fastq,2175091401.0,42648851.0,GSM4331453 r1,0:51 1:0,A:561510537;C:519609213;G:488808716;T:604683079;N:479856,51,0,,,561510537,519609213,488808716,604683079,479856,SRX7777140,SRS6196095,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.91241,,0.2128,,0.67838,,0.49729,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56854,SRR11140725,SRX7777140,SRS6196095,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,,pubmed:32703943,,KK S10,GSM4331453,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S10,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331453,GSM4331453: KK S10; Danio rerio; RNA Seq,GSM4331453,,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:GSM4331453,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S10_S10_L002_R1_001.fastq.gz,fastq,2240964531.0,43940481.0,GSM4331453 r2,0:51 1:0,A:578576709;C:535423337;G:503303427;T:623307627;N:353431,51,0,,,578576709,535423337,503303427,623307627,353431,SRX7777140,SRS6196095,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.91556,,0.21671,,0.6802,,0.48625,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56855,SRR11140722,SRX7777139,SRS6196094,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,,pubmed:32703943,,KK S9,GSM4331452,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S9,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331452,GSM4331452: KK S9; Danio rerio; RNA Seq,GSM4331452,,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:GSM4331452,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S9_S9_L001_R1_001.fastq.gz,fastq,1611443532.0,31596932.0,GSM4331452 r1,0:51 1:0,A:410991075;C:386776974;G:365779604;T:447544279;N:351600,51,0,,,410991075,386776974,365779604,447544279,351600,SRX7777139,SRS6196094,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92012,,0.16508,,0.67627,,0.48239,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56856,SRR11140723,SRX7777139,SRS6196094,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,,pubmed:32703943,,KK S9,GSM4331452,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S9,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331452,GSM4331452: KK S9; Danio rerio; RNA Seq,GSM4331452,,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:GSM4331452,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S9_S9_L002_R1_001.fastq.gz,fastq,1656004425.0,32470675.0,GSM4331452 r2,0:51 1:0,A:422384502;C:397532879;G:375660541;T:460165146;N:261357,51,0,,,422384502,397532879,375660541,460165146,261357,SRX7777139,SRS6196094,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92219,,0.16904,,0.67848,,0.48402,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56857,SRR11140720,SRX7777138,SRS6196093,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,,pubmed:32703943,,KK S8,GSM4331451,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S8,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331451,GSM4331451: KK S8; Danio rerio; RNA Seq,GSM4331451,,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:GSM4331451,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S8_S8_L001_R1_001.fastq.gz,fastq,1934862633.0,37938483.0,GSM4331451 r1,0:51 1:0,A:499654011;C:456972931;G:437085923;T:540722747;N:427021,51,0,,,499654011,456972931,437085923,540722747,427021,SRX7777138,SRS6196093,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.91412,,0.18288,,0.6756,,0.47934,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56858,SRR11140721,SRX7777138,SRS6196093,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,,pubmed:32703943,,KK S8,GSM4331451,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S8,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331451,GSM4331451: KK S8; Danio rerio; RNA Seq,GSM4331451,,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:GSM4331451,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S8_S8_L002_R1_001.fastq.gz,fastq,1980313017.0,38829667.0,GSM4331451 r2,0:51 1:0,A:511422120;C:467840244;G:447006305;T:553730531;N:313817,51,0,,,511422120,467840244,447006305,553730531,313817,SRX7777138,SRS6196093,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.9163,,0.18683,,0.67789,,0.4825,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56859,SRR11140718,SRX7777137,SRS6196103,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,,pubmed:32703943,,KK S7,GSM4331450,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S7,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331450,GSM4331450: KK S7; Danio rerio; RNA Seq,GSM4331450,,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:GSM4331450,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S7_S7_L001_R1_001.fastq.gz,fastq,2212765560.0,43387560.0,GSM4331450 r1,0:51 1:0,A:564747736;C:531775038;G:502504993;T:613239993;N:497800,51,0,,,564747736,531775038,502504993,613239993,497800,SRX7777137,SRS6196103,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.91766,,0.18575,,0.68834,,0.49253,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56860,SRR11140719,SRX7777137,SRS6196103,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,,pubmed:32703943,,KK S7,GSM4331450,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S7,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331450,GSM4331450: KK S7; Danio rerio; RNA Seq,GSM4331450,,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:GSM4331450,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S7_S7_L002_R1_001.fastq.gz,fastq,2281371015.0,44732765.0,GSM4331450 r2,0:51 1:0,A:582260042;C:548460936;G:517754644;T:632531557;N:363836,51,0,,,582260042,548460936,517754644,632531557,363836,SRX7777137,SRS6196103,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92006,,0.18635,,0.68822,,0.49366,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56861,SRR11140716,SRX7777136,SRS6196100,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,,pubmed:32703943,,KK S6,GSM4331449,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S6,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331449,GSM4331449: KK S6; Danio rerio; RNA Seq,GSM4331449,,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:GSM4331449,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S6_S6_L001_R1_001.fastq.gz,fastq,1538408268.0,30164868.0,GSM4331449 r1,0:51 1:0,A:386599261;C:379529575;G:352139755;T:419806296;N:333381,51,0,,,386599261,379529575,352139755,419806296,333381,SRX7777136,SRS6196100,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92163,,0.18919,,0.69104,,0.50313,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56862,SRR11140717,SRX7777136,SRS6196100,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,,pubmed:32703943,,KK S6,GSM4331449,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf KO,KK S6,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf KO,GSM4331449,GSM4331449: KK S6; Danio rerio; RNA Seq,GSM4331449,,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:GSM4331449,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S6_S6_L002_R1_001.fastq.gz,fastq,1578755847.0,30955997.0,GSM4331449 r2,0:51 1:0,A:396670286;C:389635536;G:361231347;T:430970090;N:248588,51,0,,,396670286,389635536,361231347,430970090,248588,SRX7777136,SRS6196100,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92301,,0.18911,,0.69205,,0.50197,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56863,SRR11140714,SRX7777135,SRS6196092,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,,pubmed:32703943,,KK S5,GSM4331448,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf type,KK S5,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf type,GSM4331448,GSM4331448: KK S5; Danio rerio; RNA Seq,GSM4331448,,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:GSM4331448,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S5_S5_L001_R1_001.fastq.gz,fastq,1933087374.0,37903674.0,GSM4331448 r1,0:51 1:0,A:488703374;C:471859383;G:442561735;T:529538057;N:424825,51,0,,,488703374,471859383,442561735,529538057,424825,SRX7777135,SRS6196092,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92283,,0.17417,,0.68235,,0.49656,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56864,SRR11140715,SRX7777135,SRS6196092,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,,pubmed:32703943,,KK S5,GSM4331448,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf type,KK S5,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf type,GSM4331448,GSM4331448: KK S5; Danio rerio; RNA Seq,GSM4331448,,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:GSM4331448,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S5_S5_L002_R1_001.fastq.gz,fastq,1979726364.0,38818164.0,GSM4331448 r2,0:51 1:0,A:500496724;C:483355860;G:452973842;T:542586288;N:313650,51,0,,,500496724,483355860,452973842,542586288,313650,SRX7777135,SRS6196092,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92466,,0.17592,,0.68112,,0.49142,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56865,SRR11140712,SRX7777134,SRS6196089,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,,pubmed:32703943,,KK S4,GSM4331447,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf type,KK S4,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf type,GSM4331447,GSM4331447: KK S4; Danio rerio; RNA Seq,GSM4331447,,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:GSM4331447,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S4_S4_L001_R1_001.fastq.gz,fastq,2048717022.0,40170922.0,GSM4331447 r1,0:51 1:0,A:520777535;C:496433068;G:465039825;T:566020770;N:445824,51,0,,,520777535,496433068,465039825,566020770,445824,SRX7777134,SRS6196089,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92114,,0.16433,,0.6812,,0.48618,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56866,SRR11140713,SRX7777134,SRS6196089,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,,pubmed:32703943,,KK S4,GSM4331447,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf type,KK S4,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf type,GSM4331447,GSM4331447: KK S4; Danio rerio; RNA Seq,GSM4331447,,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:GSM4331447,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S4_S4_L002_R1_001.fastq.gz,fastq,2107255689.0,41318739.0,GSM4331447 r2,0:51 1:0,A:535772635;C:510666072;G:477884803;T:582599966;N:332213,51,0,,,535772635,510666072,477884803,582599966,332213,SRX7777134,SRS6196089,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92263,,0.16558,,0.68183,,0.48847,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56867,SRR11140710,SRX7777133,SRS6196091,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,,pubmed:32703943,,KK S3,GSM4331446,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf type,KK S3,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf type,GSM4331446,GSM4331446: KK S3; Danio rerio; RNA Seq,GSM4331446,,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:GSM4331446,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S3_S3_L001_R1_001.fastq.gz,fastq,1686816942.0,33074842.0,GSM4331446 r1,0:51 1:0,A:420176049;C:415752484;G:390250166;T:460272173;N:366070,51,0,,,420176049,415752484,390250166,460272173,366070,SRX7777133,SRS6196091,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.9279,,0.16947,,0.68532,,0.49323,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56868,SRR11140711,SRX7777133,SRS6196091,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,,pubmed:32703943,,KK S3,GSM4331446,,tissue:embryo head|sample type:embryo head 2dpf|developmental stage:2 dpf type,KK S3,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf type,GSM4331446,GSM4331446: KK S3; Danio rerio; RNA Seq,GSM4331446,,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:GSM4331446,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP250312,,,KK-S3_S3_L002_R1_001.fastq.gz,fastq,1737614574.0,34070874.0,GSM4331446 r2,0:51 1:0,A:432907237;C:428335841;G:401665412;T:474428519;N:277565,51,0,,,432907237,428335841,401665412,474428519,277565,SRX7777133,SRS6196091,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92909,,0.1677,,0.68536,,0.49478,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System
56869,SRR11140708,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,,pubmed:32703943,,KK S2,GSM4331445,,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’ 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 ≥10 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,,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.,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°C until 2 dpf.,sample type:embryo head 2dpf|developmental stage:2 dpf type,GSM4331445,GSM4331445: KK S2; Danio rerio; RNA Seq,GSM4331445,,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,,SRP250312,,,KK-S2_S2_L001_R1_001.fastq.gz,fastq,1656733164.0,32484964.0,GSM4331445 r1,0:51 1:0,A:413061199;C:406325405;G:382881805;T:454145865;N:318890,51,0,,,413061199,406325405,382881805,454145865,318890,SRX7777132,SRS6196090,SRA1045975,GEO,"Advanced Center for Translational and Genetic Medicine (ACT-GeM), Ann & Robert H Lurie Children's Hospital of Chicago",1,0.92705,,0.1574,,0.6882,,0.4946,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-02-21,Hatching,Embryo,Head,Nervous System