{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation = \"Head\"", "rows": [[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", null, "pubmed:39289367", null, "head  scarb2a mut  rep 3", "GSM8339369", null, "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", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "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, null, null, 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, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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", null, "pubmed:39289367", null, "head  scarb2a mut  rep 2", "GSM8339368", null, "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", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "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, null, null, 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, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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", null, "pubmed:39289367", null, "head  scarb2a mut  rep 1", "GSM8339367", null, "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", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "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, null, null, 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, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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", null, "pubmed:39289367", null, "head  wt  rep 4", "GSM8339366", null, "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", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "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, null, null, 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, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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", null, "pubmed:39289367", null, "head  wt  rep 3", "GSM8339365", null, "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", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "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, null, null, 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, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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", null, "pubmed:39289367", null, "head  wt  rep 1", "GSM8339364", null, "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", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "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 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l 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 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "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, null, null, 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, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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.", null, null, null, "WT sc 2dpf", "WT sc 2dpf S1 L003", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP523914", null, null, "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, null, null, 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", null, "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.", null, null, null, "RFC1 KO sc 2dpf", "RFC1 KO sc 2dpf S2 L003", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP523914", null, null, "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, null, null, 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", null, "Canada", "2024-08-02", "Hatching", "Embryo", "Head", "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep5", "GSM3488843", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488843", "GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq", "GSM3488843", null, "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", null, "SRP170713", null, null, "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, null, null, 271859663, 271742909, 255256859, 305383003, 111107, "SRX5062217", "SRS4078157", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92793, null, 0.15706, null, 0.6686, null, 0.48785, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep5", "GSM3488843", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488843", "GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq", "GSM3488843", null, "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", null, "SRP170713", null, null, "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, null, null, 272582305, 272363181, 255837702, 306158767, 119380, "SRX5062217", "SRS4078157", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.9291, null, 0.15688, null, 0.66939, null, 0.4874, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep5", "GSM3488843", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488843", "GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq", "GSM3488843", null, "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", null, "SRP170713", null, null, "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, null, null, 272751963, 272598901, 256278919, 306301107, 114847, "SRX5062217", "SRS4078157", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92569, null, 0.15636, null, 0.67107, null, 0.48848, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep4", "GSM3488842", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488842", "GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq", "GSM3488842", null, "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", null, "SRP170713", null, null, "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, null, null, 250914585, 242617209, 230819870, 282467195, 101375, "SRX5062216", "SRS4078156", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92511, null, 0.14656, null, 0.66255, null, 0.4737, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep4", "GSM3488842", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488842", "GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq", "GSM3488842", null, "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", null, "SRP170713", null, null, "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, null, null, 252043979, 243615191, 231854021, 283736741, 109087, "SRX5062216", "SRS4078156", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92626, null, 0.14636, null, 0.66113, null, 0.47444, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep4", "GSM3488842", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488842", "GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq", "GSM3488842", null, "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", null, "SRP170713", null, null, "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, null, null, 252575184, 244090867, 232476280, 284156056, 104814, "SRX5062216", "SRS4078156", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92435, null, 0.14732, null, 0.66178, null, 0.47364, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep3", "GSM3488841", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488841", "GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq", "GSM3488841", null, "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", null, "SRP170713", null, null, "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, null, null, 242678169, 243280763, 232480047, 276234852, 98152, "SRX5062215", "SRS4078155", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.93015, null, 0.13516, null, 0.66338, null, 0.47268, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep3", "GSM3488841", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488841", "GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq", "GSM3488841", null, "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", null, "SRP170713", null, null, "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, null, null, 244193037, 244754957, 233915568, 277991308, 106269, "SRX5062215", "SRS4078155", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92992, null, 0.13363, null, 0.66143, null, 0.47596, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep3", "GSM3488841", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488841", "GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq", "GSM3488841", null, "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", null, "SRP170713", null, null, "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, null, null, 244687169, 245305809, 234523016, 278381509, 102004, "SRX5062215", "SRS4078155", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92775, null, 0.13351, null, 0.66143, null, 0.46661, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep2", "GSM3488840", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488840", "GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq", "GSM3488840", null, "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", null, "SRP170713", null, null, "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, null, null, 298212594, 304802527, 286549620, 339221142, 123938, "SRX5062214", "SRS4078154", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92713, null, 0.14665, null, 0.66547, null, 0.49543, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep2", "GSM3488840", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488840", "GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq", "GSM3488840", null, "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", null, "SRP170713", null, null, "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, null, null, 299963399, 306522449, 288138725, 341187728, 135520, "SRX5062214", "SRS4078154", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92688, null, 0.14676, null, 0.66669, null, 0.49493, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep2", "GSM3488840", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488840", "GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq", "GSM3488840", null, "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", null, "SRP170713", null, null, "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, null, null, 300016555, 306493432, 288334228, 341035993, 129323, "SRX5062214", "SRS4078154", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92486, null, 0.1456, null, 0.66576, null, 0.49558, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep1", "GSM3488839", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488839", "GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq", "GSM3488839", null, "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", null, "SRP170713", null, null, "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, null, null, 271017299, 263543757, 249256774, 306999426, 110280, "SRX5062213", "SRS4078153", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92359, null, 0.15259, null, 0.65662, null, 0.47976, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep1", "GSM3488839", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488839", "GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq", "GSM3488839", null, "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", null, "SRP170713", null, null, "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, null, null, 272497776, 264812949, 250461572, 308534070, 118408, "SRX5062213", "SRS4078153", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92537, null, 0.15294, null, 0.6564, null, 0.48091, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 Cas9 rep1", "GSM3488839", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488839", "GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq", "GSM3488839", null, "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", null, "SRP170713", null, null, "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, null, null, 272640711, 265014569, 250849083, 308618948, 113435, "SRX5062213", "SRS4078153", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92126, null, 0.15288, null, 0.65758, null, 0.48139, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep5", "GSM3488838", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488838", "GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq", "GSM3488838", null, "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", null, "SRP170713", null, null, "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, null, null, 275932434, 266759397, 253066873, 312409285, 110563, "SRX5062212", "SRS4078152", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92384, null, 0.15395, null, 0.65981, null, 0.47171, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep5", "GSM3488838", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488838", "GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq", "GSM3488838", null, "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", null, "SRP170713", null, null, "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, null, null, 277089394, 267821306, 254016353, 313757990, 120932, "SRX5062212", "SRS4078152", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92569, null, 0.15411, null, 0.66042, null, 0.47795, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep5", "GSM3488838", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488838", "GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq", "GSM3488838", null, "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", null, "SRP170713", null, null, "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, null, null, 277244311, 268029085, 254374324, 313812352, 114626, "SRX5062212", "SRS4078152", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92312, null, 0.15403, null, 0.66131, null, 0.475, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep4", "GSM3488837", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488837", "GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq", "GSM3488837", null, "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", null, "SRP170713", null, null, "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, null, null, 244142324, 238841091, 227525215, 278701440, 98844, "SRX5062211", "SRS4078151", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92369, null, 0.14203, null, 0.66107, null, 0.47606, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep4", "GSM3488837", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488837", "GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq", "GSM3488837", null, "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", null, "SRP170713", null, null, "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, null, null, 245733399, 240305756, 228973873, 280447377, 107586, "SRX5062211", "SRS4078151", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.9253, null, 0.14267, null, 0.66156, null, 0.47641, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep4", "GSM3488837", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488837", "GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq", "GSM3488837", null, "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", null, "SRP170713", null, null, "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, null, null, 245728339, 240375764, 229145692, 280334702, 101610, "SRX5062211", "SRS4078151", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.9222, null, 0.1414, null, 0.66129, null, 0.47546, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep3", "GSM3488836", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488836", "GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq", "GSM3488836", null, "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", null, "SRP170713", null, null, "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, null, null, 306283941, 302350915, 285978262, 345570234, 122368, "SRX5062210", "SRS4078150", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92431, null, 0.15332, null, 0.6664, null, 0.48826, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep3", "GSM3488836", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488836", "GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq", "GSM3488836", null, "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", null, "SRP170713", null, null, "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, null, null, 307334069, 303294657, 286891055, 346690285, 132967, "SRX5062210", "SRS4078150", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92593, null, 0.15367, null, 0.66604, null, 0.4866, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep3", "GSM3488836", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488836", "GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq", "GSM3488836", null, "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", null, "SRP170713", null, null, "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, null, null, 307763481, 303768183, 287566818, 347039016, 126246, "SRX5062210", "SRS4078150", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92279, null, 0.15465, null, 0.6662, null, 0.48909, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep2", "GSM3488835", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488835", "GSM3488835: ncapg2 gRNA3 rep2; Danio rerio; RNA Seq", "GSM3488835", null, "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", null, "SRP170713", null, null, "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, null, null, 256902869, 258344237, 242502701, 289217725, 103982, "SRX5062209", "SRS4078149", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92959, null, 0.1635, null, 0.66647, null, 0.49696, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep2", "GSM3488835", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488835", "GSM3488835: ncapg2 gRNA3 rep2; Danio rerio; RNA Seq", "GSM3488835", null, "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", null, "SRP170713", null, null, "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, null, null, 257964459, 259432490, 243475655, 290506674, 112202, "SRX5062209", "SRS4078149", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.93114, null, 0.16334, null, 0.66849, null, 0.49762, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep2", "GSM3488835", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488835", "GSM3488835: ncapg2 gRNA3 rep2; Danio rerio; RNA Seq", "GSM3488835", null, "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", null, "SRP170713", null, null, "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, null, null, 258264531, 259707847, 243893492, 290716219, 106514, "SRX5062209", "SRS4078149", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92874, null, 0.16404, null, 0.666, null, 0.50389, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep1", "GSM3488834", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488834", "GSM3488834: ncapg2 gRNA3 rep1; Danio rerio; RNA Seq", "GSM3488834", null, "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", null, "SRP170713", null, null, "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, null, null, 289846111, 297515045, 276860101, 327344773, 120217, "SRX5062208", "SRS4078148", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92975, null, 0.17522, null, 0.66302, null, 0.50487, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep1", "GSM3488834", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488834", "GSM3488834: ncapg2 gRNA3 rep1; Danio rerio; RNA Seq", "GSM3488834", null, "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", null, "SRP170713", null, null, "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, null, null, 291794226, 299402070, 278615395, 329608144, 130153, "SRX5062208", "SRS4078148", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.93135, null, 0.17445, null, 0.66123, null, 0.50823, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "ncapg2 gRNA3 rep1", "GSM3488834", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf", "GSM3488834", "GSM3488834: ncapg2 gRNA3 rep1; Danio rerio; RNA Seq", "GSM3488834", null, "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", null, "SRP170713", null, null, "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, null, null, 291514396, 299035235, 278501070, 329123391, 124560, "SRX5062208", "SRS4078148", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92761, null, 0.17518, null, 0.66332, null, 0.5075, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep5", "GSM3488833", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488833", "GSM3488833: phenol red rep5; Danio rerio; RNA Seq", "GSM3488833", null, "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", null, "SRP170713", null, null, "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, null, null, 286238785, 282775459, 266662113, 324177455, 114515, "SRX5062207", "SRS4078147", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92591, null, 0.15107, null, 0.66511, null, 0.48651, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep5", "GSM3488833", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488833", "GSM3488833: phenol red rep5; Danio rerio; RNA Seq", "GSM3488833", null, "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", null, "SRP170713", null, null, "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, null, null, 288194571, 284729076, 268455130, 326485683, 124025, "SRX5062207", "SRS4078147", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92677, null, 0.15299, null, 0.66486, null, 0.48959, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep5", "GSM3488833", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488833", "GSM3488833: phenol red rep5; Danio rerio; RNA Seq", "GSM3488833", null, "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", null, "SRP170713", null, null, "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, null, null, 288662075, 285050661, 268977814, 326667234, 119391, "SRX5062207", "SRS4078147", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92353, null, 0.15263, null, 0.66371, null, 0.48436, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep4", "GSM3488832", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488832", "GSM3488832: phenol red rep4; Danio rerio; RNA Seq", "GSM3488832", null, "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", null, "SRP170713", null, null, "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, null, null, 224888320, 228719312, 214749825, 254159559, 88590, "SRX5062206", "SRS4078146", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92938, null, 0.16094, null, 0.66949, null, 0.49837, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep4", "GSM3488832", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488832", "GSM3488832: phenol red rep4; Danio rerio; RNA Seq", "GSM3488832", null, "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", null, "SRP170713", null, null, "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, null, null, 226207683, 229941498, 215897068, 255669930, 95558, "SRX5062206", "SRS4078146", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.9298, null, 0.16225, null, 0.66977, null, 0.49705, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep4", "GSM3488832", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488832", "GSM3488832: phenol red rep4; Danio rerio; RNA Seq", "GSM3488832", null, "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", null, "SRP170713", null, null, "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, null, null, 226705927, 230492844, 216518196, 256121312, 90468, "SRX5062206", "SRS4078146", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92696, null, 0.1594, null, 0.66906, null, 0.49888, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep3", "GSM3488831", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488831", "GSM3488831: phenol red rep3; Danio rerio; RNA Seq", "GSM3488831", null, "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", null, "SRP170713", null, null, "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, null, null, 221202889, 218769075, 206704109, 250396873, 89117, "SRX5062205", "SRS4078145", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92557, null, 0.151, null, 0.6618, null, 0.48267, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep3", "GSM3488831", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488831", "GSM3488831: phenol red rep3; Danio rerio; RNA Seq", "GSM3488831", null, "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", null, "SRP170713", null, null, "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, null, null, 221806455, 219590198, 207296255, 251287886, 96276, "SRX5062205", "SRS4078145", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92893, null, 0.15176, null, 0.6648, null, 0.48203, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep3", "GSM3488831", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488831", "GSM3488831: phenol red rep3; Danio rerio; RNA Seq", "GSM3488831", null, "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", null, "SRP170713", null, null, "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, null, null, 222335986, 220068562, 207953397, 251675877, 92887, "SRX5062205", "SRS4078145", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92511, null, 0.15132, null, 0.66332, null, 0.48892, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep2", "GSM3488830", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488830", "GSM3488830: phenol red rep2; Danio rerio; RNA Seq", "GSM3488830", null, "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", null, "SRP170713", null, null, "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, null, null, 217899984, 213724390, 202494755, 248901144, 87057, "SRX5062204", "SRS4078143", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.9212, null, 0.13988, null, 0.65951, null, 0.47797, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep2", "GSM3488830", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488830", "GSM3488830: phenol red rep2; Danio rerio; RNA Seq", "GSM3488830", null, "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", null, "SRP170713", null, null, "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, null, null, 219288459, 214987628, 203666399, 250368228, 93476, "SRX5062204", "SRS4078143", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92249, null, 0.14008, null, 0.65833, null, 0.46889, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep2", "GSM3488830", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488830", "GSM3488830: phenol red rep2; Danio rerio; RNA Seq", "GSM3488830", null, "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", null, "SRP170713", null, null, "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, null, null, 219700893, 215424116, 204218333, 250727670, 89669, "SRX5062204", "SRS4078143", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92091, null, 0.13895, null, 0.65977, null, 0.47244, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep1", "GSM3488829", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488829", "GSM3488829: phenol red rep1; Danio rerio; RNA Seq", "GSM3488829", null, "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", null, "SRP170713", null, null, "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, null, null, 217088547, 211224249, 199952646, 245380769, 86860, "SRX5062203", "SRS4078144", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.924, null, 0.15017, null, 0.6495, null, 0.47585, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep1", "GSM3488829", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488829", "GSM3488829: phenol red rep1; Danio rerio; RNA Seq", "GSM3488829", null, "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", null, "SRP170713", null, null, "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, null, null, 218155528, 212129394, 200837990, 246501710, 94456, "SRX5062203", "SRS4078144", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92461, null, 0.14859, null, 0.6491, null, 0.47655, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:30609410", null, "phenol red rep1", "GSM3488829", null, "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\u2019 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", null, "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\u2019s 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\u00b0C until 2 dpf.", "tissue:embryo head|time point:2 dpf red", "GSM3488829", "GSM3488829: phenol red rep1; Danio rerio; RNA Seq", "GSM3488829", null, "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", null, "SRP170713", null, null, "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, null, null, 218561820, 212596855, 201358917, 246893407, 90274, "SRX5062203", "SRS4078144", "SRA814826", "GEO", "Center for Human Disease Modeling, Duke University Medical Center", 1, 0.92318, null, 0.14661, null, 0.6491, null, 0.47527, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-11-26", "Hatching", "Embryo", "Head", "Nervous System"], [50953, "SRR8383314", "SRX5193232", "SRS4199232", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e6", "GSM3536476", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536476", "GSM3536476: 3 primemRNAseq zPCF11deltaPAS1 hom e6; Danio rerio; RNA Seq", "GSM3536476", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536476", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GCTCGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 170117572.0, 1936836.0, "GSM3536476 r1", "0:87.83", "A:57043415;C:29867475;G:33401453;T:49804679;N:550", 87, null, null, null, 57043415, 29867475, 33401453, 49804679, 550, "SRX5193232", "SRS4199232", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82781, null, 0.11752, null, 0.7791, null, 0.51275, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50954, "SRR8383315", "SRX5193232", "SRS4199232", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e6", "GSM3536476", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536476", "GSM3536476: 3 primemRNAseq zPCF11deltaPAS1 hom e6; Danio rerio; RNA Seq", "GSM3536476", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536476", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GCTCGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 175173536.0, 1995191.0, "GSM3536476 r2", "0:87.80", "A:58844991;C:30708254;G:34327735;T:51292146;N:410", 87, null, null, null, 58844991, 30708254, 34327735, 51292146, 410, "SRX5193232", "SRS4199232", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82604, null, 0.11764, null, 0.78029, null, 0.51756, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50955, "SRR8383312", "SRX5193231", "SRS4199231", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e5", "GSM3536475", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536475", "GSM3536475: 3 primemRNAseq zPCF11deltaPAS1 hom e5; Danio rerio; RNA Seq", "GSM3536475", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536475", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CAAGCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 606360323.0, 6905543.0, "GSM3536475 r1", "0:87.81", "A:198106425;C:109559199;G:122893662;T:175799225;N:1812", 87, null, null, null, 198106425, 109559199, 122893662, 175799225, 1812, "SRX5193231", "SRS4199231", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.8427, null, 0.1325, null, 0.78879, null, 0.51921, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50956, "SRR8383313", "SRX5193231", "SRS4199231", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e5", "GSM3536475", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536475", "GSM3536475: 3 primemRNAseq zPCF11deltaPAS1 hom e5; Danio rerio; RNA Seq", "GSM3536475", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536475", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CAAGCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 624201360.0, 7110625.0, "GSM3536475 r2", "0:87.78", "A:204175038;C:112645351;G:126392625;T:180986966;N:1380", 87, null, null, null, 204175038, 112645351, 126392625, 180986966, 1380, "SRX5193231", "SRS4199231", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84211, null, 0.13385, null, 0.7895, null, 0.52023, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50957, "SRR8383310", "SRX5193230", "SRS4199230", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e4", "GSM3536474", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536474", "GSM3536474: 3 primemRNAseq zPCF11deltaPAS1 hom e4; Danio rerio; RNA Seq", "GSM3536474", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536474", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_AACGCCATC.bam.fastq_trimmed.fastq.gz", "fastq", 892780335.0, 10219904.0, "GSM3536474 r1", "0:87.36", "A:300258267;C:163189097;G:178114941;T:251215317;N:2713", 87, null, null, null, 300258267, 163189097, 178114941, 251215317, 2713, "SRX5193230", "SRS4199230", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83419, null, 0.14585, null, 0.80255, null, 0.50109, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50958, "SRR8383311", "SRX5193230", "SRS4199230", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e4", "GSM3536474", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536474", "GSM3536474: 3 primemRNAseq zPCF11deltaPAS1 hom e4; Danio rerio; RNA Seq", "GSM3536474", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536474", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_AACGCCATC.bam.fastq_trimmed.fastq.gz", "fastq", 921074852.0, 10547533.0, "GSM3536474 r2", "0:87.33", "A:310174374;C:168106596;G:183538421;T:259253357;N:2104", 87, null, null, null, 310174374, 168106596, 183538421, 259253357, 2104, "SRX5193230", "SRS4199230", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83245, null, 0.14487, null, 0.80359, null, 0.50415, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50959, "SRR8383308", "SRX5193229", "SRS4199229", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e3", "GSM3536473", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536473", "GSM3536473: 3 primemRNAseq zPCF11deltaPAS1 hom e3; Danio rerio; RNA Seq", "GSM3536473", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536473", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TTTATGATC.bam.fastq_trimmed.fastq.gz", "fastq", 1018559174.0, 11616470.0, "GSM3536473 r1", "0:87.68", "A:347433965;C:179438057;G:202582370;T:289101606;N:3176", 87, null, null, null, 347433965, 179438057, 202582370, 289101606, 3176, "SRX5193229", "SRS4199229", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81678, null, 0.16376, null, 0.79295, null, 0.52685, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50960, "SRR8383309", "SRX5193229", "SRS4199229", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e3", "GSM3536473", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536473", "GSM3536473: 3 primemRNAseq zPCF11deltaPAS1 hom e3; Danio rerio; RNA Seq", "GSM3536473", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536473", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TTTATGATC.bam.fastq_trimmed.fastq.gz", "fastq", 1049029756.0, 11967431.0, "GSM3536473 r2", "0:87.66", "A:358315722;C:184586479;G:208348099;T:297777016;N:2440", 87, null, null, null, 358315722, 184586479, 208348099, 297777016, 2440, "SRX5193229", "SRS4199229", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81613, null, 0.16396, null, 0.7931, null, 0.51637, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50961, "SRR8383306", "SRX5193228", "SRS4199228", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e2", "GSM3536472", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536472", "GSM3536472: 3 primemRNAseq zPCF11deltaPAS1 hom e2; Danio rerio; RNA Seq", "GSM3536472", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536472", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CCGCAAATC.bam.fastq_trimmed.fastq.gz", "fastq", 95347510.0, 1083083.0, "GSM3536472 r1", "0:88.03", "A:31277905;C:16917301;G:19217962;T:27934061;N:281", 88, null, null, null, 31277905, 16917301, 19217962, 27934061, 281, "SRX5193228", "SRS4199228", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84359, null, 0.1281, null, 0.77849, null, 0.50658, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50962, "SRR8383307", "SRX5193228", "SRS4199228", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e2", "GSM3536472", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536472", "GSM3536472: 3 primemRNAseq zPCF11deltaPAS1 hom e2; Danio rerio; RNA Seq", "GSM3536472", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536472", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CCGCAAATC.bam.fastq_trimmed.fastq.gz", "fastq", 98289209.0, 1116653.0, "GSM3536472 r2", "0:88.02", "A:32271861;C:17428261;G:19780092;T:28808779;N:216", 88, null, null, null, 32271861, 17428261, 19780092, 28808779, 216, "SRX5193228", "SRS4199228", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84257, null, 0.12826, null, 0.77881, null, 0.51159, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50963, "SRR8383304", "SRX5193227", "SRS4199227", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e1", "GSM3536471", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536471", "GSM3536471: 3 primemRNAseq zPCF11deltaPAS1 hom e1; Danio rerio; RNA Seq", "GSM3536471", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536471", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CACACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 151964150.0, 1729761.0, "GSM3536471 r1", "0:87.85", "A:51182251;C:27047472;G:29597244;T:44136727;N:456", 87, null, null, null, 51182251, 27047472, 29597244, 44136727, 456, "SRX5193227", "SRS4199227", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83286, null, 0.13372, null, 0.78023, null, 0.44685, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50964, "SRR8383305", "SRX5193227", "SRS4199227", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e1", "GSM3536471", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536471", "GSM3536471: 3 primemRNAseq zPCF11deltaPAS1 hom e1; Danio rerio; RNA Seq", "GSM3536471", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536471", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CACACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 156746824.0, 1784420.0, "GSM3536471 r2", "0:87.84", "A:52870952;C:27860644;G:30505998;T:45508859;N:371", 87, null, null, null, 52870952, 27860644, 30505998, 45508859, 371, "SRX5193227", "SRS4199227", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83111, null, 0.13281, null, 0.78001, null, 0.44609, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50965, "SRR8383302", "SRX5193226", "SRS4199226", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e5", "GSM3536470", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536470", "GSM3536470: 3 primemRNAseq zPCF11deltaPAS1 het e5; Danio rerio; RNA Seq", "GSM3536470", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536470", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TACCTTATC.bam.fastq_trimmed.fastq.gz", "fastq", 132241407.0, 1505632.0, "GSM3536470 r1", "0:87.83", "A:44701797;C:23272762;G:25927608;T:38338866;N:374", 87, null, null, null, 44701797, 23272762, 25927608, 38338866, 374, "SRX5193226", "SRS4199226", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82845, null, 0.13469, null, 0.7767, null, 0.52442, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50966, "SRR8383303", "SRX5193226", "SRS4199226", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e5", "GSM3536470", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536470", "GSM3536470: 3 primemRNAseq zPCF11deltaPAS1 het e5; Danio rerio; RNA Seq", "GSM3536470", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536470", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TACCTTATC.bam.fastq_trimmed.fastq.gz", "fastq", 136234092.0, 1551581.0, "GSM3536470 r2", "0:87.80", "A:46139985;C:23944780;G:26663569;T:39485404;N:354", 87, null, null, null, 46139985, 23944780, 26663569, 39485404, 354, "SRX5193226", "SRS4199226", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82629, null, 0.13474, null, 0.7794, null, 0.51749, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50967, "SRR8383300", "SRX5193225", "SRS4199225", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e4", "GSM3536469", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536469", "GSM3536469: 3 primemRNAseq zPCF11deltaPAS1 het e4; Danio rerio; RNA Seq", "GSM3536469", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536469", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_ATGAACATC.bam.fastq_trimmed.fastq.gz", "fastq", 219395486.0, 2496420.0, "GSM3536469 r1", "0:87.88", "A:74049072;C:38996524;G:43402255;T:62946930;N:705", 87, null, null, null, 74049072, 38996524, 43402255, 62946930, 705, "SRX5193225", "SRS4199225", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83282, null, 0.14125, null, 0.78474, null, 0.5102, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50968, "SRR8383301", "SRX5193225", "SRS4199225", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e4", "GSM3536469", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536469", "GSM3536469: 3 primemRNAseq zPCF11deltaPAS1 het e4; Danio rerio; RNA Seq", "GSM3536469", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536469", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_ATGAACATC.bam.fastq_trimmed.fastq.gz", "fastq", 225177913.0, 2562839.0, "GSM3536469 r2", "0:87.86", "A:76113440;C:39951108;G:44487323;T:64625459;N:583", 87, null, null, null, 76113440, 39951108, 44487323, 64625459, 583, "SRX5193225", "SRS4199225", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82913, null, 0.13953, null, 0.78681, null, 0.50967, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50969, "SRR8383298", "SRX5193224", "SRS4199224", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e3", "GSM3536468", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536468", "GSM3536468: 3 primemRNAseq zPCF11deltaPAS1 het e3; Danio rerio; RNA Seq", "GSM3536468", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536468", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TTAACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 499775526.0, 5688628.0, "GSM3536468 r1", "0:87.86", "A:163216421;C:88556243;G:100895279;T:147106087;N:1496", 87, null, null, null, 163216421, 88556243, 100895279, 147106087, 1496, "SRX5193224", "SRS4199224", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84129, null, 0.13912, null, 0.78194, null, 0.5187, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50970, "SRR8383299", "SRX5193224", "SRS4199224", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e3", "GSM3536468", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536468", "GSM3536468: 3 primemRNAseq zPCF11deltaPAS1 het e3; Danio rerio; RNA Seq", "GSM3536468", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536468", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TTAACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 514657493.0, 5859797.0, "GSM3536468 r2", "0:87.83", "A:168321204;C:91084703;G:103742599;T:151507844;N:1143", 87, null, null, null, 168321204, 91084703, 103742599, 151507844, 1143, "SRX5193224", "SRS4199224", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83984, null, 0.1389, null, 0.78291, null, 0.51811, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50971, "SRR8383296", "SRX5193223", "SRS4199223", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e2", "GSM3536467", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536467", "GSM3536467: 3 primemRNAseq zPCF11deltaPAS1 het e2; Danio rerio; RNA Seq", "GSM3536467", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536467", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CGGTTAATC.bam.fastq_trimmed.fastq.gz", "fastq", 628544705.0, 7145719.0, "GSM3536467 r1", "0:87.96", "A:208540640;C:110628846;G:124026622;T:185346588;N:2009", 87, null, null, null, 208540640, 110628846, 124026622, 185346588, 2009, "SRX5193223", "SRS4199223", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83647, null, 0.11358, null, 0.7821, null, 0.50973, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50972, "SRR8383297", "SRX5193223", "SRS4199223", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e2", "GSM3536467", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536467", "GSM3536467: 3 primemRNAseq zPCF11deltaPAS1 het e2; Danio rerio; RNA Seq", "GSM3536467", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536467", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CGGTTAATC.bam.fastq_trimmed.fastq.gz", "fastq", 647232214.0, 7359619.0, "GSM3536467 r2", "0:87.94", "A:215025740;C:113794072;G:127525437;T:190885451;N:1514", 87, null, null, null, 215025740, 113794072, 127525437, 190885451, 1514, "SRX5193223", "SRS4199223", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83376, null, 0.11387, null, 0.78305, null, 0.51943, null, 79, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50973, "SRR8383294", "SRX5193222", "SRS4199222", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e1", "GSM3536466", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536466", "GSM3536466: 3 primemRNAseq zPCF11deltaPAS1 het e1; Danio rerio; RNA Seq", "GSM3536466", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536466", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TCAGGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 789817010.0, 8990777.0, "GSM3536466 r1", "0:87.85", "A:255721217;C:143531700;G:162243420;T:228318196;N:2477", 87, null, null, null, 255721217, 143531700, 162243420, 228318196, 2477, "SRX5193222", "SRS4199222", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85167, null, 0.14197, null, 0.78813, null, 0.51648, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50974, "SRR8383295", "SRX5193222", "SRS4199222", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e1", "GSM3536466", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536466", "GSM3536466: 3 primemRNAseq zPCF11deltaPAS1 het e1; Danio rerio; RNA Seq", "GSM3536466", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536466", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TCAGGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 812333266.0, 9249708.0, "GSM3536466 r2", "0:87.82", "A:263342967;C:147474874;G:166670966;T:234842610;N:1849", 87, null, null, null, 263342967, 147474874, 166670966, 234842610, 1849, "SRX5193222", "SRS4199222", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85028, null, 0.14374, null, 0.78754, null, 0.51112, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50975, "SRR8383292", "SRX5193221", "SRS4199221", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e3", "GSM3536465", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536465", "GSM3536465: 3 primemRNAseq zPCF11deltaPAS1 wt e3; Danio rerio; RNA Seq", "GSM3536465", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536465", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GGCTGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 164145508.0, 1870416.0, "GSM3536465 r1", "0:87.76", "A:53096508;C:29983980;G:33483503;T:47581048;N:469", 87, null, null, null, 53096508, 29983980, 33483503, 47581048, 469, "SRX5193221", "SRS4199221", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85271, null, 0.13713, null, 0.78626, null, 0.42953, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50976, "SRR8383293", "SRX5193221", "SRS4199221", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e3", "GSM3536465", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536465", "GSM3536465: 3 primemRNAseq zPCF11deltaPAS1 wt e3; Danio rerio; RNA Seq", "GSM3536465", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536465", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GGCTGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 168774555.0, 1923679.0, "GSM3536465 r2", "0:87.74", "A:54636127;C:30795817;G:34408599;T:48933579;N:433", 87, null, null, null, 54636127, 30795817, 34408599, 48933579, 433, "SRX5193221", "SRS4199221", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85284, null, 0.136, null, 0.78595, null, 0.51852, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50977, "SRR8383290", "SRX5193220", "SRS4199220", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e2", "GSM3536464", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536464", "GSM3536464: 3 primemRNAseq zPCF11deltaPAS1 wt e2; Danio rerio; RNA Seq", "GSM3536464", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536464", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_AATCCGATC.bam.fastq_trimmed.fastq.gz", "fastq", 237761677.0, 2716138.0, "GSM3536464 r1", "0:87.54", "A:77086804;C:43323233;G:48823094;T:68527734;N:812", 87, null, null, null, 77086804, 43323233, 48823094, 68527734, 812, "SRX5193220", "SRS4199220", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84891, null, 0.16038, null, 0.78839, null, 0.53051, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50978, "SRR8383291", "SRX5193220", "SRS4199220", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e2", "GSM3536464", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536464", "GSM3536464: 3 primemRNAseq zPCF11deltaPAS1 wt e2; Danio rerio; RNA Seq", "GSM3536464", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536464", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_AATCCGATC.bam.fastq_trimmed.fastq.gz", "fastq", 244669202.0, 2795847.0, "GSM3536464 r2", "0:87.51", "A:79391766;C:44532003;G:50184304;T:70560584;N:545", 87, null, null, null, 79391766, 44532003, 50184304, 70560584, 545, "SRX5193220", "SRS4199220", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84722, null, 0.16156, null, 0.79011, null, 0.53158, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50979, "SRR8383288", "SRX5193219", "SRS4199219", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e1", "GSM3536463", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536463", "GSM3536463: 3 primemRNAseq zPCF11deltaPAS1 wt e1; Danio rerio; RNA Seq", "GSM3536463", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536463", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CCTAAGATC.bam.fastq_trimmed.fastq.gz", "fastq", 129332543.0, 1472338.0, "GSM3536463 r1", "0:87.84", "A:43564845;C:22890586;G:25561204;T:37315459;N:449", 87, null, null, null, 43564845, 22890586, 25561204, 37315459, 449, "SRX5193219", "SRS4199219", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83187, null, 0.13547, null, 0.78234, null, 0.52271, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50980, "SRR8383289", "SRX5193219", "SRS4199219", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e1", "GSM3536463", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536463", "GSM3536463: 3 primemRNAseq zPCF11deltaPAS1 wt e1; Danio rerio; RNA Seq", "GSM3536463", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536463", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CCTAAGATC.bam.fastq_trimmed.fastq.gz", "fastq", 133356093.0, 1518522.0, "GSM3536463 r2", "0:87.82", "A:44962657;C:23585729;G:26335793;T:38471613;N:301", 87, null, null, null, 44962657, 23585729, 26335793, 38471613, 301, "SRX5193219", "SRS4199219", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83065, null, 0.13598, null, 0.78378, null, 0.53247, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50981, "SRR8383286", "SRX5193218", "SRS4199218", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e6", "GSM3536462", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536462", "GSM3536462: 3 primemRNAseq zPCF11null hom e6; Danio rerio; RNA Seq", "GSM3536462", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536462", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TCGAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 685570157.0, 7880276.0, "GSM3536462 r1", "0:87.00", "A:220749091;C:129576519;G:144120777;T:191121622;N:2148", 87, null, null, null, 220749091, 129576519, 144120777, 191121622, 2148, "SRX5193218", "SRS4199218", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82107, null, 0.23078, null, 0.81941, null, 0.59068, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50982, "SRR8383287", "SRX5193218", "SRS4199218", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e6", "GSM3536462", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536462", "GSM3536462: 3 primemRNAseq zPCF11null hom e6; Danio rerio; RNA Seq", "GSM3536462", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536462", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TCGAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 704276360.0, 8098980.0, "GSM3536462 r2", "0:86.96", "A:227042988;C:132957237;G:147852510;T:196421958;N:1667", 86, null, null, null, 227042988, 132957237, 147852510, 196421958, 1667, "SRX5193218", "SRS4199218", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81976, null, 0.23195, null, 0.82014, null, 0.58764, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50983, "SRR8383284", "SRX5193217", "SRS4199217", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e5", "GSM3536461", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536461", "GSM3536461: 3 primemRNAseq zPCF11null hom e5; Danio rerio; RNA Seq", "GSM3536461", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GTGCCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 770954082.0, 8859450.0, "GSM3536461 r1", "0:87.02", "A:257152925;C:141557495;G:158071178;T:214170140;N:2344", 87, null, null, null, 257152925, 141557495, 158071178, 214170140, 2344, "SRX5193217", "SRS4199217", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80635, null, 0.19837, null, 0.81355, null, 0.40061, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50984, "SRR8383285", "SRX5193217", "SRS4199217", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e5", "GSM3536461", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536461", "GSM3536461: 3 primemRNAseq zPCF11null hom e5; Danio rerio; RNA Seq", "GSM3536461", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GTGCCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 792682872.0, 9113148.0, "GSM3536461 r2", "0:86.98", "A:264818153;C:145303306;G:162291530;T:220268109;N:1774", 86, null, null, null, 264818153, 145303306, 162291530, 220268109, 1774, "SRX5193217", "SRS4199217", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80446, null, 0.1978, null, 0.81397, null, 0.57793, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50985, "SRR8383282", "SRX5193216", "SRS4199216", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e4", "GSM3536460", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536460", "GSM3536460: 3 primemRNAseq zPCF11null hom e4; Danio rerio; RNA Seq", "GSM3536460", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536460", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_AATAGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 128394352.0, 1469184.0, "GSM3536460 r1", "0:87.39", "A:41878409;C:23656471;G:26363280;T:36495822;N:370", 87, null, null, null, 41878409, 23656471, 26363280, 36495822, 370, "SRX5193216", "SRS4199216", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.8404, null, 0.20794, null, 0.81635, null, 0.57453, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50986, "SRR8383283", "SRX5193216", "SRS4199216", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e4", "GSM3536460", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536460", "GSM3536460: 3 primemRNAseq zPCF11null hom e4; Danio rerio; RNA Seq", "GSM3536460", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536460", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_AATAGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 131964907.0, 1510456.0, "GSM3536460 r2", "0:87.37", "A:43071448;C:24301835;G:27045591;T:37545716;N:317", 87, null, null, null, 43071448, 24301835, 27045591, 37545716, 317, "SRX5193216", "SRS4199216", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84091, null, 0.21002, null, 0.8168, null, 0.57732, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50987, "SRR8383280", "SRX5193215", "SRS4199215", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e3", "GSM3536459", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536459", "GSM3536459: 3 primemRNAseq zPCF11null hom e3; Danio rerio; RNA Seq", "GSM3536459", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536459", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GCATGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 198921603.0, 2281764.0, "GSM3536459 r1", "0:87.18", "A:67933819;C:36044297;G:40047977;T:54894929;N:581", 87, null, null, null, 67933819, 36044297, 40047977, 54894929, 581, "SRX5193215", "SRS4199215", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80512, null, 0.21831, null, 0.81856, null, 0.58328, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50988, "SRR8383281", "SRX5193215", "SRS4199215", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e3", "GSM3536459", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536459", "GSM3536459: 3 primemRNAseq zPCF11null hom e3; Danio rerio; RNA Seq", "GSM3536459", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536459", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GCATGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 204339172.0, 2344861.0, "GSM3536459 r2", "0:87.14", "A:69852605;C:36969411;G:41077998;T:56438756;N:402", 87, null, null, null, 69852605, 36969411, 41077998, 56438756, 402, "SRX5193215", "SRS4199215", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80367, null, 0.21762, null, 0.81858, null, 0.58312, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50989, "SRR8383278", "SRX5193214", "SRS4199214", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e2", "GSM3536458", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536458", "GSM3536458: 3 primemRNAseq zPCF11null hom e2; Danio rerio; RNA Seq", "GSM3536458", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CTCCATATC.bam.fastq_trimmed.fastq.gz", "fastq", 243678478.0, 2785241.0, "GSM3536458 r1", "0:87.49", "A:80921391;C:44962028;G:49483835;T:68310471;N:753", 87, null, null, null, 80921391, 44962028, 49483835, 68310471, 753, "SRX5193214", "SRS4199214", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.8288, null, 0.19506, null, 0.82674, null, 0.5695, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50990, "SRR8383279", "SRX5193214", "SRS4199214", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e2", "GSM3536458", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536458", "GSM3536458: 3 primemRNAseq zPCF11null hom e2; Danio rerio; RNA Seq", "GSM3536458", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CTCCATATC.bam.fastq_trimmed.fastq.gz", "fastq", 251121623.0, 2871387.0, "GSM3536458 r2", "0:87.46", "A:83477676;C:46277942;G:50927013;T:70438422;N:570", 87, null, null, null, 83477676, 46277942, 50927013, 70438422, 570, "SRX5193214", "SRS4199214", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82553, null, 0.19377, null, 0.82674, null, 0.56696, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50991, "SRR8383276", "SRX5193213", "SRS4199213", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e1", "GSM3536457", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536457", "GSM3536457: 3 primemRNAseq zPCF11null hom e1; Danio rerio; RNA Seq", "GSM3536457", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536457", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TAGGCTATC.bam.fastq_trimmed.fastq.gz", "fastq", 125156975.0, 1440450.0, "GSM3536457 r1", "0:86.89", "A:41125276;C:23385340;G:26101084;T:34544902;N:373", 86, null, null, null, 41125276, 23385340, 26101084, 34544902, 373, "SRX5193213", "SRS4199213", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82681, null, 0.23851, null, 0.82162, null, 0.59477, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50992, "SRR8383277", "SRX5193213", "SRS4199213", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e1", "GSM3536457", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536457", "GSM3536457: 3 primemRNAseq zPCF11null hom e1; Danio rerio; RNA Seq", "GSM3536457", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536457", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TAGGCTATC.bam.fastq_trimmed.fastq.gz", "fastq", 128831164.0, 1483314.0, "GSM3536457 r2", "0:86.85", "A:42399550;C:24025044;G:26817005;T:35589296;N:269", 86, null, null, null, 42399550, 24025044, 26817005, 35589296, 269, "SRX5193213", "SRS4199213", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82598, null, 0.23646, null, 0.82207, null, 0.59052, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50993, "SRR8383274", "SRX5193212", "SRS4199212", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e4", "GSM3536456", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536456", "GSM3536456: 3 primemRNAseq zPCF11null het e4; Danio rerio; RNA Seq", "GSM3536456", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536456", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CGAAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 118253929.0, 1353894.0, "GSM3536456 r1", "0:87.34", "A:41106016;C:21057430;G:23427525;T:32662627;N:331", 87, null, null, null, 41106016, 21057430, 23427525, 32662627, 331, "SRX5193212", "SRS4199212", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81195, null, 0.18309, null, 0.82191, null, 0.55215, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50994, "SRR8383275", "SRX5193212", "SRS4199212", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e4", "GSM3536456", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536456", "GSM3536456: 3 primemRNAseq zPCF11null het e4; Danio rerio; RNA Seq", "GSM3536456", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536456", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CGAAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 121725680.0, 1394241.0, "GSM3536456 r2", null, null, null, null, null, null, null, null, null, null, null, "SRX5193212", "SRS4199212", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.76785, null, 0.17246, null, 0.81962, null, 0.55625, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50995, "SRR8383272", "SRX5193211", "SRS4199211", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e3", "GSM3536455", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536455", "GSM3536455: 3 primemRNAseq zPCF11null het e3; Danio rerio; RNA Seq", "GSM3536455", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536455", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_ACCTACATC.bam.fastq_trimmed.fastq.gz", "fastq", 186888249.0, 2140393.0, "GSM3536455 r1", "0:87.31", "A:65786002;C:32923065;G:36796601;T:51382007;N:574", 87, null, null, null, 65786002, 32923065, 36796601, 51382007, 574, "SRX5193211", "SRS4199211", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80995, null, 0.19928, null, 0.8033, null, 0.5594, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50996, "SRR8383273", "SRX5193211", "SRS4199211", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e3", "GSM3536455", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536455", "GSM3536455: 3 primemRNAseq zPCF11null het e3; Danio rerio; RNA Seq", "GSM3536455", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536455", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_ACCTACATC.bam.fastq_trimmed.fastq.gz", "fastq", 192642130.0, 2206994.0, "GSM3536455 r2", "0:87.29", "A:67912529;C:33877053;G:37899068;T:52953002;N:478", 87, null, null, null, 67912529, 33877053, 37899068, 52953002, 478, "SRX5193211", "SRS4199211", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80759, null, 0.19797, null, 0.80348, null, 0.55867, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50997, "SRR8383270", "SRX5193210", "SRS4199210", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e2", "GSM3536454", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536454", "GSM3536454: 3 primemRNAseq zPCF11null het e2; Danio rerio; RNA Seq", "GSM3536454", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536454", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TGGATTATC.bam.fastq_trimmed.fastq.gz", "fastq", 198506304.0, 2271548.0, "GSM3536454 r1", "0:87.39", "A:65363370;C:36248554;G:40646664;T:56247077;N:639", 87, null, null, null, 65363370, 36248554, 40646664, 56247077, 639, "SRX5193210", "SRS4199210", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81892, null, 0.1808, null, 0.81558, null, 0.55265, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50998, "SRR8383271", "SRX5193210", "SRS4199210", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e2", "GSM3536454", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536454", "GSM3536454: 3 primemRNAseq zPCF11null het e2; Danio rerio; RNA Seq", "GSM3536454", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536454", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TGGATTATC.bam.fastq_trimmed.fastq.gz", "fastq", 204546039.0, 2341528.0, "GSM3536454 r2", "0:87.36", "A:67442570;C:37300418;G:41843482;T:57959051;N:518", 87, null, null, null, 67442570, 37300418, 41843482, 57959051, 518, "SRX5193210", "SRS4199210", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81597, null, 0.18014, null, 0.81714, null, 0.55071, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50999, "SRR8383268", "SRX5193209", "SRS4199209", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e1", "GSM3536453", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536453", "GSM3536453: 3 primemRNAseq zPCF11null het e1; Danio rerio; RNA Seq", "GSM3536453", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536453", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GCGAATATC.bam.fastq_trimmed.fastq.gz", "fastq", 166454199.0, 1896918.0, "GSM3536453 r1", "0:87.75", "A:54362704;C:30210406;G:33769933;T:48110651;N:505", 87, null, null, null, 54362704, 30210406, 33769933, 48110651, 505, "SRX5193209", "SRS4199209", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83471, null, 0.17434, null, 0.80231, null, 0.55417, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 172, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation_coarse\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Embryo", "p1": "Head"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Head", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 172, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Head&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", 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