Down regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_E8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_H3 are compared to EHMT1_WT_E8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from EHMT1_Ter_H3/G3/E1_cells_[RNA-seq] compared to EHMT1_WT_F8/E9/E8_cells_[RNA-seq]
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). RNAseq expression values from down regulated genes from EHMT1_Ter_H3/G3/E1_cells_[RNA-seq] are compared to EHMT1_WT_F8/E9/E8_cells_[RNA-seq]. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from EHMT1_Ter_H3/G3/E1_cells_[RNA-seq] compared to EHMT1_WT_F8/E9/E8_cells_[RNA-seq]
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). RNAseq expression values from up regulated genes from EHMT1_Ter_H3/G3/E1_cells_[RNA-seq] are compared to EHMT1_WT_F8/E9/E8_cells_[RNA-seq]. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_H3 are compared to EHMT1_WT_F8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes from EHMT1_Ter_H3 are compared to EHMT1_WT_F8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_G3 are compared to EHMT1_WT_F8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_G3 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes of EHMT1_Ter_G3 are compared to EHMT1_WT_F8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_WT_E9 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes of two WT controls, EHMT1_WT_E9 compared to EHMT1_WT_F8 clone line are shown. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_WT_E9 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes of two WT controls, EHMT1_WT_E9 compared to EHMT1_WT_F8 clone line are shown. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_Ter_E1 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_E1 are compared to EHMT1_WT_F8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_E1 compared to EHMT1_WT_F8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes from EHMT1_Ter_E1 are compared to EHMT1_WT_F8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_E8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes from EHMT1_Ter_H3 are compared to EHMT1_WT_E8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_E8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_0776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_E1 are compared to EHMT1_WT_E8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_E1 compared to EHMT1_WT_E8
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes from EHMT1_Ter_E1 are compared to EHMT1_WT_E8 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_E9
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_H3 are compared to EHMT1_WT_E9 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_H3 compared to EHMT1_WT_E9
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes from EHMT1_Ter_H3 are compared to EHMT1_WT_E9 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_Ter_G3 compared to EHMT1_WT_E9
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_G3 are compared to EHMT1_WT_E9 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_G3 compared to EHMT1_WT_E9
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes from EHMT1_Ter_G3 are compared to EHMT1_WT_E9 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Down regulated genes from CLLAG of EHMT1_Ter_E1 compared to EHMT1_WT_E9
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from down regulated genes from EHMT1_Ter_E1 are compared to EHMT1_WT_E9 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Up regulated genes from CLLAG of EHMT1_Ter_E1 compared to EHMT1_WT_E9
Description:
The introduction of a premature stop codon in the EHMT1 gene results in EHMT1 haploinsufficiency, a phenotype known to cause Kleefstra Syndrome. To create EHMT1 haploinsufficiency, the EHMT1_Ter variant was introduced into Human Embryonic Kidney 293 T (HEK293T) cells using CRISPR/Cas9 ribonucleoprotein complex transfection. Single cell clones were generated and gDNA analysed by high-throughput EHMT1 amplicon sequencing for the selection of three clones with the EHMT1 wild-type (EHMT1_WT; E8, E9, F8), and three clones that were heterozygous for EHMT1 truncation (EHMT1_Ter; E1, G3, H3; NG_011776.1: g.203511_203520del, p.Pro114). Cap dependent linker ligation analysis of gene expression (CLLAG) from up regulated genes from EHMT1_Ter_E1 are compared to EHMT1_WT_E9 clone lines. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP279927. Cell Line Ontology CLO:0001230.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E Jones, Alistair Rr Forrest, Gareth Baynam, Timo Lassmann
Dysregulation of NRSF/REST via EHMT1 is associated with psychiatric disorders and Kleefstra syndrome, Z scores
Description:
EHMT1 is an epigenetic repressor that is causal for Kleefstra Syndrome (KS), a neurodevelopmental disorder (NDD) leading to intelectual disability, and is associated with schizophrenia. Here, the researchers aim to show we show that reduced EHMT1 activity decreases NRSF/REST protein leading to abnormal neuronal gene expression and progression of neurodevelopment in human iPSC. Five induced pluripotent stem cell samples (from fibroblasts of adult, male, skin) were used. The stem cells were gifted from: Lieber Institute for Brain Development, Johns Hopkins Medical Campus. Total RNA extracted from a control hiPSC line and control cells treated for 72h with various concentrations of UNC0638 i.e 50, 100, 200 or 250nM as a model for Kleefstra syndrome. Polyadenylated adaptors were ligated to the 3′-end, 5′-adaptors were then ligated, and the resulting RNAs were reverse transcribed to generate cDNA that can be amplified by PCR. The amplified product was run on low range ultra agarose in TBE buffer and a size-selection was performed to ensure that the cDNA used for sequencing primarily contains miRNAs rather than other RNA contaminants. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and Z scores calculated. Genes were annotated as Ensembl gene ids. SRA Study id ERP130338.
Up regulated genes from NPC_EHMT1_SNV compared to NPC_EHMT1_WT
Description:
A Kleefstra Syndrome patient’s known pathogenic EHMT1 genetic variant, EHMT1_c.3430C > T; p.Gln1144* (referred to as EHMT1_SNV) was introduced into iPSCs by CRISPR single base editing, followed by neuronal cell differentiation. IPSCs were induced for neural differentiation to form neural progenitor cells (NPCs). Kleefstra syndrome is caused by EHMT1 haploinsufficiency that results in partial or complete loss of EHMT1 expression. Expression was compared in NPCs between NPC_EHMT1_SNV and NPC_EHMT1_WT. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP325023. Experimental Factor Ontology EFO:EFO_0010976; KOLF2-C1.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Sarra Jamieson, Michelle Ward, Gareth Baynam, Timo Lassmann
Down regulated genes from NPC_WT compared to iPSC_WT
Description:
A Kleefstra Syndrome patient’s known pathogenic EHMT1 genetic variant, EHMT1_c.3430C > T; p.Gln1144* (referred to as EHMT1_SNV) was introduced into iPSCs by CRISPR single base editing, followed by neuronal cell differentiation. IPSCs were induced for neural differentiation to form neural progenitor cells (NPCs). Kleefstra syndrome is caused by EHMT1 haploinsufficiency that results in partial or complete loss of EHMT1 expression. Expression was compared between NPC_WT and iPSC_WT respectively. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP325023. Experimental Factor Ontology EFO:EFO_0010976; KOLF2-C1.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Sarra Jamieson, Michelle Ward, Gareth Baynam, Timo Lassmann
Up regulated genes from NPC_WT compared to iPSC_WT
Description:
A Kleefstra Syndrome patient’s known pathogenic EHMT1 genetic variant, EHMT1_c.3430C > T; p.Gln1144* (referred to as EHMT1_SNV) was introduced into iPSCs by CRISPR single base editing, followed by neuronal cell differentiation. IPSCs were induced for neural differentiation to form neural progenitor cells (NPCs). Kleefstra syndrome is caused by EHMT1 haploinsufficiency that results in partial or complete loss of EHMT1 expression. Expression was compared between NPC_WT and iPSC_WT respectively. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP325023. Experimental Factor Ontology EFO:EFO_0010976; KOLF2-C1.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Sarra Jamieson, Michelle Ward, Gareth Baynam, Timo Lassmann
Down regulated genes from NPC_SNV compared to iPSC_SNV
Description:
A Kleefstra Syndrome patient’s known pathogenic EHMT1 genetic variant, EHMT1_c.3430C > T; p.Gln1144* (referred to as EHMT1_SNV) was introduced into iPSCs by CRISPR single base editing, followed by neuronal cell differentiation. IPSCs were induced for neural differentiation to form neural progenitor cells (NPCs). Kleefstra syndrome is caused by EHMT1 haploinsufficiency that results in partial or complete loss of EHMT1 expression. Expression was compared between NPC_SNV and iPSC_SNV respectively. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP325023. Experimental Factor Ontology EFO:EFO_0010976; KOLF2-C1.
Authors:
Vanessa S Fear, Catherine A Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Sarra Jamieson, Michelle Ward, Gareth Baynam, Timo Lassmann
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