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genome wide rna seq analysis  (Broad Clinical Labs)
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Broad Clinical Labs genome wide rna seq analysis
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Genome Wide Rna Seq Analysis, supplied by Broad Clinical Labs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genome-wide rna-seq data of zebrafish embryos at 3 dpf  (Ebiogen Inc)
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Ebiogen Inc genome-wide rna-seq data of zebrafish embryos at 3 dpf
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Genome Wide Rna Seq Data Of Zebrafish Embryos At 3 Dpf, supplied by Ebiogen Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genome-wide rna-seq data  (Ebiogen Inc)
90
Ebiogen Inc genome-wide rna-seq data
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Genome Wide Rna Seq Data, supplied by Ebiogen Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genome-wide rna-seq data - by Bioz Stars, 2026-07
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rna-seq genome-wide approach  (Illumina Inc)
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Illumina Inc rna-seq genome-wide approach
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Rna Seq Genome Wide Approach, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genome-wide distribution of rna-seq reads  (Novogene)
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Novogene genome-wide distribution of rna-seq reads
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Genome Wide Distribution Of Rna Seq Reads, supplied by Novogene, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genome-wide distribution of rna-seq reads - by Bioz Stars, 2026-07
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genome-wide chromatin immunoprecipitation-sequencing (chip-seq) and rna-seq data  (Epigenomics ag)
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Epigenomics ag genome-wide chromatin immunoprecipitation-sequencing (chip-seq) and rna-seq data
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Genome Wide Chromatin Immunoprecipitation Sequencing (Chip Seq) And Rna Seq Data, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genome wide rna-seq  (Illumina Inc)
90
Illumina Inc genome wide rna-seq
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Genome Wide Rna Seq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genome wide rna-seq - by Bioz Stars, 2026-07
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rna-seq and genome-wide transcriptome analyses  (Novogene)
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Novogene rna-seq and genome-wide transcriptome analyses
Figure 3. High levels of mutant HTT specificity supported <t>by</t> <t>RNA-seq</t> analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.
Rna Seq And Genome Wide Transcriptome Analyses, supplied by Novogene, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Figure 3. High levels of mutant HTT specificity supported by RNA-seq analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.

Journal: Molecular therapy. Methods & clinical development

Article Title: PAM-altering SNP-based allele-specific CRISPR-Cas9 therapeutic strategies for Huntington's disease.

doi: 10.1016/j.omtm.2022.08.005

Figure Lengend Snippet: Figure 3. High levels of mutant HTT specificity supported by RNA-seq analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.

Article Snippet: Then, genome-wide RNA-seq analysis was performed by the Broad Institute.

Techniques: Mutagenesis, RNA Sequencing, Expressing, CRISPR, Sequencing

Figure 4. On-target gene specificity supported by RNA-seq analysis To increase the sensitivity and the power to detect any small but significantly altered genes, we combined 10 targeted clonal lines targeted by L4-R4 and 10 clonal lines targeted by L4-R6 gRNA combinations to be compared with 12 EV-treated controls. (A) Significance values (un- corrected p values on the y axis) were compared with log2 (fold-change) (x axis) to highlight significantly altered genes. A horizontal and a vertical line represent Bonfer- roni-corrected significance and zero fold-change, respectively. (B) Expression levels of total HTT (mutant plus normal) based on the DGE analysis are summarized in a boxplot. Total HTT levels were decreased by 38% in TP-CRISPR targeted clonal lines.

Journal: Molecular therapy. Methods & clinical development

Article Title: PAM-altering SNP-based allele-specific CRISPR-Cas9 therapeutic strategies for Huntington's disease.

doi: 10.1016/j.omtm.2022.08.005

Figure Lengend Snippet: Figure 4. On-target gene specificity supported by RNA-seq analysis To increase the sensitivity and the power to detect any small but significantly altered genes, we combined 10 targeted clonal lines targeted by L4-R4 and 10 clonal lines targeted by L4-R6 gRNA combinations to be compared with 12 EV-treated controls. (A) Significance values (un- corrected p values on the y axis) were compared with log2 (fold-change) (x axis) to highlight significantly altered genes. A horizontal and a vertical line represent Bonfer- roni-corrected significance and zero fold-change, respectively. (B) Expression levels of total HTT (mutant plus normal) based on the DGE analysis are summarized in a boxplot. Total HTT levels were decreased by 38% in TP-CRISPR targeted clonal lines.

Article Snippet: Then, genome-wide RNA-seq analysis was performed by the Broad Institute.

Techniques: RNA Sequencing, Expressing, Mutagenesis, CRISPR