quantification of allele-specific expression by pyrosequencing (quasep)method Search Results


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Pyrosequencing Inc expression by pyrosequencing quasep
Expression By Pyrosequencing Quasep, supplied by Pyrosequencing Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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allele  (Pyrosequencing Inc)
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Pyrosequencing Inc allele
a Bar plot showing the ratio for the observed relative to the expected overlap of reactivated, full escape and late-silenced genes with high-confidence NDD genes. For reactivated genes, an intriguing accumulation of NDD genes was observed (1.43 times more than expected; P = 6.72 × 10 −3 ). P- values were determined by the cumulative distribution function. b Immunostaining of organoid sections of the different experimental lines showing SOX2 (white) and MAP2 (magenta). Scale bars = 500 µm. c Box and jitter plots showing the quantification of the fraction of MAP2 in neural tissue (SOX2 + MAP2+ area) on d30 (M-ctrl, n = 36; M-OS/het, n = 39; M-OS/male, n = 34; M-OS/maleR, n = 25; J-ctrl, n = 9; J-OS/het, n = 13; J-OS/hom, n = 13; exact P values (top to bottom): 0.03, 9.7 × 10 −13 , 2.4 × 10 −9 , <2.2 × 10 −16 , 8.1 × 10 −9 , 7.9 × 10 −4 , 4.0 × 10 −6 , 4.3 × 10 −3 ). d Box and jitter plots showing the quantification of the fraction of MAP2 in neural tissue (SOX2 + MAP2+ area) on d30 in the XIST expressing A-lines (A-ctrl, n = 15; A-OS/het, n = 29; A-OS/hom, n = 28; exact P values (top to bottom): 0.035, 8 × 10 −5 , 0.032). For c , d boxplots show median, quartiles (box), and range (whiskers). In the jitter plots dots represent individual organoids. Two-sided Wilcoxon rank sum test; *P < 0.05, **P < 0.01, ***P < 0.001, ns P > 0.05. <t>e</t> <t>Allele-specific</t> RT-PCR revealing reactivation (*) of the inactive MID1 allele in brain organoids derived from the M-lines. f Reactivation (*) of the inactive MID1 allele in brain organoids derived from the J-lines as revealed by allele-specific RT-PCR. g Reactivation (*) of the inactive MID1 allele in brain organoids derived from the A-liness as revealed by allele-specific RT-PCR. Source data are provided as a file.
Allele, supplied by Pyrosequencing Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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allele - by Bioz Stars, 2026-06
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a Bar plot showing the ratio for the observed relative to the expected overlap of reactivated, full escape and late-silenced genes with high-confidence NDD genes. For reactivated genes, an intriguing accumulation of NDD genes was observed (1.43 times more than expected; P = 6.72 × 10 −3 ). P- values were determined by the cumulative distribution function. b Immunostaining of organoid sections of the different experimental lines showing SOX2 (white) and MAP2 (magenta). Scale bars = 500 µm. c Box and jitter plots showing the quantification of the fraction of MAP2 in neural tissue (SOX2 + MAP2+ area) on d30 (M-ctrl, n = 36; M-OS/het, n = 39; M-OS/male, n = 34; M-OS/maleR, n = 25; J-ctrl, n = 9; J-OS/het, n = 13; J-OS/hom, n = 13; exact P values (top to bottom): 0.03, 9.7 × 10 −13 , 2.4 × 10 −9 , <2.2 × 10 −16 , 8.1 × 10 −9 , 7.9 × 10 −4 , 4.0 × 10 −6 , 4.3 × 10 −3 ). d Box and jitter plots showing the quantification of the fraction of MAP2 in neural tissue (SOX2 + MAP2+ area) on d30 in the XIST expressing A-lines (A-ctrl, n = 15; A-OS/het, n = 29; A-OS/hom, n = 28; exact P values (top to bottom): 0.035, 8 × 10 −5 , 0.032). For c , d boxplots show median, quartiles (box), and range (whiskers). In the jitter plots dots represent individual organoids. Two-sided Wilcoxon rank sum test; *P < 0.05, **P < 0.01, ***P < 0.001, ns P > 0.05. e Allele-specific RT-PCR revealing reactivation (*) of the inactive MID1 allele in brain organoids derived from the M-lines. f Reactivation (*) of the inactive MID1 allele in brain organoids derived from the J-lines as revealed by allele-specific RT-PCR. g Reactivation (*) of the inactive MID1 allele in brain organoids derived from the A-liness as revealed by allele-specific RT-PCR. Source data are provided as a file.

Journal: Nature Communications

Article Title: Dynamic allele usage of X-linked genes ameliorates neurodevelopmental disease phenotypes in brain organoids

doi: 10.1038/s41467-026-68428-x

Figure Lengend Snippet: a Bar plot showing the ratio for the observed relative to the expected overlap of reactivated, full escape and late-silenced genes with high-confidence NDD genes. For reactivated genes, an intriguing accumulation of NDD genes was observed (1.43 times more than expected; P = 6.72 × 10 −3 ). P- values were determined by the cumulative distribution function. b Immunostaining of organoid sections of the different experimental lines showing SOX2 (white) and MAP2 (magenta). Scale bars = 500 µm. c Box and jitter plots showing the quantification of the fraction of MAP2 in neural tissue (SOX2 + MAP2+ area) on d30 (M-ctrl, n = 36; M-OS/het, n = 39; M-OS/male, n = 34; M-OS/maleR, n = 25; J-ctrl, n = 9; J-OS/het, n = 13; J-OS/hom, n = 13; exact P values (top to bottom): 0.03, 9.7 × 10 −13 , 2.4 × 10 −9 , <2.2 × 10 −16 , 8.1 × 10 −9 , 7.9 × 10 −4 , 4.0 × 10 −6 , 4.3 × 10 −3 ). d Box and jitter plots showing the quantification of the fraction of MAP2 in neural tissue (SOX2 + MAP2+ area) on d30 in the XIST expressing A-lines (A-ctrl, n = 15; A-OS/het, n = 29; A-OS/hom, n = 28; exact P values (top to bottom): 0.035, 8 × 10 −5 , 0.032). For c , d boxplots show median, quartiles (box), and range (whiskers). In the jitter plots dots represent individual organoids. Two-sided Wilcoxon rank sum test; *P < 0.05, **P < 0.01, ***P < 0.001, ns P > 0.05. e Allele-specific RT-PCR revealing reactivation (*) of the inactive MID1 allele in brain organoids derived from the M-lines. f Reactivation (*) of the inactive MID1 allele in brain organoids derived from the J-lines as revealed by allele-specific RT-PCR. g Reactivation (*) of the inactive MID1 allele in brain organoids derived from the A-liness as revealed by allele-specific RT-PCR. Source data are provided as a file.

Article Snippet: Female fibroblasts were reprogrammed into iPSCs and upon clonal selection we determined which X-chromosome is active in which clone by using Quantification of Allele-Specific Expression by Pyrosequencing (QUASEP) assays (Fig. , Supplementary Data ).

Techniques: Immunostaining, Expressing, Reverse Transcription Polymerase Chain Reaction, Derivative Assay