superscriptiii reverse transcriptase Thermo Fisher Search Results


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  • 90
    Thermo Fisher smart seq2 rt mix
    Parental haplotype reconstruction with single-cell sequencing detects genome wide allelic expression. The workflow combined high coverage exome sequencing of fetuses and mothers, used for variant calling to reconstruct the parental haplotypes for each fetus (using SNPs that are both heterozygous in the fetus and homozygous in the mother); isolation of single cells from the fetal gonad and adrenal gland, followed by RNA sequencing using <t>Smart-seq2;</t> and the alignment of the RNA reads per fetus to both parental genomes and the quantification of parental expression for all informative SNPs per haplotype
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    Thermo Fisher superscriptii reverse transcriptase
    Parental haplotype reconstruction with single-cell sequencing detects genome wide allelic expression. The workflow combined high coverage exome sequencing of fetuses and mothers, used for variant calling to reconstruct the parental haplotypes for each fetus (using SNPs that are both heterozygous in the fetus and homozygous in the mother); isolation of single cells from the fetal gonad and adrenal gland, followed by RNA sequencing using <t>Smart-seq2;</t> and the alignment of the RNA reads per fetus to both parental genomes and the quantification of parental expression for all informative SNPs per haplotype
    Superscriptii Reverse Transcriptase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2388 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher superscriptiii reverse transcriptase
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    Superscriptiii Reverse Transcriptase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher superscriptiii reverse transcriptase kit
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    Superscriptiii Reverse Transcriptase Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 121 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher superscriptii rnaseh reverse transcriptase
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    Superscriptii Rnaseh Reverse Transcriptase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 82/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher superscriptii reverse transcriptase kit
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    Superscriptii Reverse Transcriptase Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 100 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher supersciptiii reverse transcriptase
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Thermo Fisher reverse transcriptase reaction
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Thermo Fisher m mlv
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    M Mlv, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1567 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher superscriptiii rnase h reverse transcriptase
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    Superscriptiii Rnase H Reverse Transcriptase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 83/100, based on 49 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher m mulv reverse transcriptase superscriptii
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    Supersriptiii Rnase H Reverse Transcriptase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 81/100, based on 71 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
    Superscriptiii Reverse Transciptase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    78
    Thermo Fisher trancriptase superscriptii
    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and <t>three</t> resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from <t>RNA-seq</t> analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .
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    Parental haplotype reconstruction with single-cell sequencing detects genome wide allelic expression. The workflow combined high coverage exome sequencing of fetuses and mothers, used for variant calling to reconstruct the parental haplotypes for each fetus (using SNPs that are both heterozygous in the fetus and homozygous in the mother); isolation of single cells from the fetal gonad and adrenal gland, followed by RNA sequencing using Smart-seq2; and the alignment of the RNA reads per fetus to both parental genomes and the quantification of parental expression for all informative SNPs per haplotype

    Journal: Nature Communications

    Article Title: Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

    doi: 10.1038/s41467-018-04215-7

    Figure Lengend Snippet: Parental haplotype reconstruction with single-cell sequencing detects genome wide allelic expression. The workflow combined high coverage exome sequencing of fetuses and mothers, used for variant calling to reconstruct the parental haplotypes for each fetus (using SNPs that are both heterozygous in the fetus and homozygous in the mother); isolation of single cells from the fetal gonad and adrenal gland, followed by RNA sequencing using Smart-seq2; and the alignment of the RNA reads per fetus to both parental genomes and the quantification of parental expression for all informative SNPs per haplotype

    Article Snippet: Reverse transcription (RT) was performed by the addition of 5.6 µl Smart-Seq2 RT mix (0.5 µl SuperScriptII (Invitrogen Cat. 18064-014); 2 µl 5 × SuperScriptII buffer; 0.5 µl 100 mM DTT; 2 µl 5 M betaine; 0.1 µl 1 mM MgCl2 ; 0.25 µl Recombinant RNase inhibitor (TaKaRa 40U/µl Ref. 2313A); 0.1 µl 100 µM LNA strand switch primer; 0.15 µl water, per reaction) and incubation (90 min 42 °C; 10 “strand-switch” cycles of (2 min 50 °C; 2 min 70 °C); 4 °C) in a thermal cycler. cDNA amplification: cDNA amplification was performed by the addition of 15 µl of Smart-seq2 PCR mix [12.5 µl 2× KAPA HiFi HotStart ReadyMix (KAPA Biosystems Ref. KK2602); 0.25 µl 10 µM ISPCR primers; 2.25 µl water, per reaction] and incubation [3 min 98 °C; 19 cycles of (20 s (s) 98 °C; 15 s 67 °C; 6 min 72 °C); 5 min 70 °C; 4 °C] in a thermal cycler.

    Techniques: Sequencing, Genome Wide, Expressing, Variant Assay, Isolation, RNA Sequencing Assay

    Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and three resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from RNA-seq analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .

    Journal: Molecular Cell

    Article Title: Gene Resistance to Transcriptional Reprogramming following Nuclear Transfer Is Directly Mediated by Multiple Chromatin-Repressive Pathways

    doi: 10.1016/j.molcel.2017.01.030

    Figure Lengend Snippet: Multiple Chromatin Modifier Combinations Affect Resistance at a Single-Gene Level (A) Venn diagram shows the number of genes losing resistance upon four individual chromatin modifier treatments. (B) Example of digital signature of resistance obtained by differential gene expression analysis for a non-resistant ( G3pdh ) and three resistant ( Trap1A , Otx2 , and Sox2 ) genes. The digital signature indicates whether a gene is resistant (shown as 1 when the gene is differentially expressed in MEF-NT compared to ES-NT) or loses resistance (shown as 0, when the gene is not differentially expressed in MEF-NT compared to ES-NT) in each of the 12 conditions tested. The bar graphs show qRT-PCR analysis of gene expression (mean ± SEM of four samples of eight oocytes NT). (C) The numbers of genes for which a synergistic, neutral, adverse, or insensitive effect is observed when combining two chromatin modifier treatments are shown. (D) Venn diagram shows the number of genes sensitive to a histone modifier (Kdm4d, Kdm6b, or USP21) in nuclei with normal (WT) or hypomethylated DNA (Dnmt1N). (E) Loss of resistant gene sensitivity to Kdm6b in DNA-hypomethylated MEF correlates with loss of H3K27me3. The y axis indicates the number of genes that lose H3K27me3 in MEF with hypomethylated DNA compared to WT MEF. Resistant genes are split according to change in sensitivity to Kdm6b after NT when comparing WT MEF to MEF with hypomethylated DNA (red dot). The boxplot shows the background distribution of H3K27me3 change when sampling 10,000 times for a random set of genes of the same size as the resistant gene subset tested. The number in parentheses indicates a p value generated by calculating the proportion of the random background that has a more extreme value than the observed percentages from each of the three groups. (F) Heatmap illustrating the change in gene expression in normal (WT MEF nuclei) or hypomethylated DNA (Dnmt1N MEF nuclei) upon expression of histone modifiers. Ten clusters representing the main trend of gene expression change were selected based on k-means clustering of expression data from RNA-seq analysis (RPKM). The trend of change in gene expression in these ten clusters is shown in the heatmap as a Z score. See also Table S4 .

    Article Snippet: RT-qPCR Annealing of oligodT primers to the RNAs is performed by incubating at 65°C for 5min 12 μL of RNA mixed with 0.5 μL of 100 μM oligodT(15) and 0.5 μL of 10mM dNTPs followed by an incubation 5min on ice. cDNAs synthesis was performed by adding 4 μL of 5X second strand buffer, 1 μL 0.1M dTT, 1 μL H2 O, 0.5 μL RNase inhibitor, and 0.5 μL superscriptIII reverse transcriptase (InVitrogen, 18080093) to the RNA solution and incubating at 50°C for one hour.

    Techniques: Expressing, Quantitative RT-PCR, Sampling, Generated, RNA Sequencing Assay