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c643 (ATCC)

Name: c643
Brand: ATCC
Rating: 93 (19 reviews)

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ATCC c643
$a , X-chromosomal transcripts are less upregulated upon m 6 A depletion in male mESCs ( P value = 1.86 × 10 –17 , two-tailed Wilcoxon rank-sum test). The cumulative fraction of transcripts (RPKM > 1) on individual autosomes (gray) and the X chromosome (orange) that show a given expression fold change (log 2 , RNA-seq) upon m 6 A depletion (STM2457, 24 h). Mean expression changes for all autosomes are shown as a black line. Effect sizes (blue) show the shift in medians, expressed as percentage of the average interquartile range (IQR) of autosomal and X-chromosomal genes (see ). b , X:A expression ratios show a significant reduction upon m 6 A depletion ( P = 1.4 × 10 –15 , two-tailed t -test of linear contrasts in mixed effect Gaussian model in log scale). c , Differential effects on autosomal and X-chromosomal transcripts already occur after 6 h of m 6 A depletion. Median fold changes (log 2 ) of transcripts from autosomes ( n = 19, gray) and the X chromosome ( n = 1, orange) estimated by RNA-seq at different time points of m 6 A depletion (STM2457, 3, 6, 9 and 12 h). Boxes represent quartiles, center lines denote medians, and whiskers extend to most extreme values within 1.5 × interquartile range. d , Same as a , for human primary fibroblasts (STM2457, 9 h). P value = 6.24 × 10 –6 , two-tailed Wilcoxon rank-sum test. Effect sizes are shown as the shift in medians of the two distributions, expressed as percentage of the average IQR of autosomal and X-chromosomal genes (see ). e , Same as b , for human cell lines ( P value = 0.0000803 (human fibroblasts), P value = 0.0000379 (HEK293T), P value = 0.0003284 <t>(C643),</t> P value = 0.0002982 (RPE1). P values were calculated as in a , with multiple testing correction.$
C643, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/c643/product/ATCC
Average 93 stars, based on 19 article reviews

c643 - by Bioz Stars, 2026-02

93/100 stars

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1) Product Images from "RNA stability controlled by m 6 A methylation contributes to X-to-autosome dosage compensation in mammals"

Article Title: RNA stability controlled by m 6 A methylation contributes to X-to-autosome dosage compensation in mammals

Journal: Nature Structural & Molecular Biology

doi: 10.1038/s41594-023-00997-7

$a , X-chromosomal transcripts are less upregulated upon m 6 A depletion in male mESCs ( P value = 1.86 × 10 –17 , two-tailed Wilcoxon rank-sum test). The cumulative fraction of transcripts (RPKM > 1) on individual autosomes (gray) and the X chromosome (orange) that show a given expression fold change (log 2 , RNA-seq) upon m 6 A depletion (STM2457, 24 h). Mean expression changes for all autosomes are shown as a black line. Effect sizes (blue) show the shift in medians, expressed as percentage of the average interquartile range (IQR) of autosomal and X-chromosomal genes (see ). b , X:A expression ratios show a significant reduction upon m 6 A depletion ( P = 1.4 × 10 –15 , two-tailed t -test of linear contrasts in mixed effect Gaussian model in log scale). c , Differential effects on autosomal and X-chromosomal transcripts already occur after 6 h of m 6 A depletion. Median fold changes (log 2 ) of transcripts from autosomes ( n = 19, gray) and the X chromosome ( n = 1, orange) estimated by RNA-seq at different time points of m 6 A depletion (STM2457, 3, 6, 9 and 12 h). Boxes represent quartiles, center lines denote medians, and whiskers extend to most extreme values within 1.5 × interquartile range. d , Same as a , for human primary fibroblasts (STM2457, 9 h). P value = 6.24 × 10 –6 , two-tailed Wilcoxon rank-sum test. Effect sizes are shown as the shift in medians of the two distributions, expressed as percentage of the average IQR of autosomal and X-chromosomal genes (see ). e , Same as b , for human cell lines ( P value = 0.0000803 (human fibroblasts), P value = 0.0000379 (HEK293T), P value = 0.0003284 (C643), P value = 0.0002982 (RPE1). P values were calculated as in a , with multiple testing correction.$
Figure Legend Snippet: a , X-chromosomal transcripts are less upregulated upon m 6 A depletion in male mESCs ( P value = 1.86 × 10 –17 , two-tailed Wilcoxon rank-sum test). The cumulative fraction of transcripts (RPKM > 1) on individual autosomes (gray) and the X chromosome (orange) that show a given expression fold change (log 2 , RNA-seq) upon m 6 A depletion (STM2457, 24 h). Mean expression changes for all autosomes are shown as a black line. Effect sizes (blue) show the shift in medians, expressed as percentage of the average interquartile range (IQR) of autosomal and X-chromosomal genes (see ). b , X:A expression ratios show a significant reduction upon m 6 A depletion ( P = 1.4 × 10 –15 , two-tailed t -test of linear contrasts in mixed effect Gaussian model in log scale). c , Differential effects on autosomal and X-chromosomal transcripts already occur after 6 h of m 6 A depletion. Median fold changes (log 2 ) of transcripts from autosomes ( n = 19, gray) and the X chromosome ( n = 1, orange) estimated by RNA-seq at different time points of m 6 A depletion (STM2457, 3, 6, 9 and 12 h). Boxes represent quartiles, center lines denote medians, and whiskers extend to most extreme values within 1.5 × interquartile range. d , Same as a , for human primary fibroblasts (STM2457, 9 h). P value = 6.24 × 10 –6 , two-tailed Wilcoxon rank-sum test. Effect sizes are shown as the shift in medians of the two distributions, expressed as percentage of the average IQR of autosomal and X-chromosomal genes (see ). e , Same as b , for human cell lines ( P value = 0.0000803 (human fibroblasts), P value = 0.0000379 (HEK293T), P value = 0.0003284 (C643), P value = 0.0002982 (RPE1). P values were calculated as in a , with multiple testing correction.

Techniques Used: Two Tailed Test, Expressing, RNA Sequencing

$a . Principal component analyses for replicates of RNA-seq experiments under m 6 A-depleted and control conditions for human primary fibroblasts (STM2457, 9 h), HEK293T cells, C643 cells and RPE1 cells (STM2457, 24 h). Replicate number given next to each data point. b . X-chromosomal transcripts show significantly lower fold changes upon m 6 A depletion than autosomal transcripts ( P value = 6.92e-06 [HEK293T, n = 12,856 of autosomal transcripts, n = 443 of X-chromosomal transcripts], P value = 4.53e-05 [C643, n = 11,109 of autosomal transcripts, n = 383 of X-chromosomal transcripts], P value = 0.0001901 [RPE1, n = 10,732 of autosomal transcripts, n = 347 of X-chromosomal transcripts], Wilcoxon rank-sum test). Cumulative fraction of transcripts on individual autosomes (grey) and the X chromosome (orange) that show a given fold change (log 2 ) in m 6 A-depleted (STM2457, 24 h) over control conditions for HEK293T, C643, and RPE1 cells. Mean expression changes for all autosomes are shown as black line. Effect sizes (blue) shown the shift in medians, expressed as percent of the average IQR of autosomal and X-chromosomal genes (see ).$
Figure Legend Snippet: a . Principal component analyses for replicates of RNA-seq experiments under m 6 A-depleted and control conditions for human primary fibroblasts (STM2457, 9 h), HEK293T cells, C643 cells and RPE1 cells (STM2457, 24 h). Replicate number given next to each data point. b . X-chromosomal transcripts show significantly lower fold changes upon m 6 A depletion than autosomal transcripts ( P value = 6.92e-06 [HEK293T, n = 12,856 of autosomal transcripts, n = 443 of X-chromosomal transcripts], P value = 4.53e-05 [C643, n = 11,109 of autosomal transcripts, n = 383 of X-chromosomal transcripts], P value = 0.0001901 [RPE1, n = 10,732 of autosomal transcripts, n = 347 of X-chromosomal transcripts], Wilcoxon rank-sum test). Cumulative fraction of transcripts on individual autosomes (grey) and the X chromosome (orange) that show a given fold change (log 2 ) in m 6 A-depleted (STM2457, 24 h) over control conditions for HEK293T, C643, and RPE1 cells. Mean expression changes for all autosomes are shown as black line. Effect sizes (blue) shown the shift in medians, expressed as percent of the average IQR of autosomal and X-chromosomal genes (see ).

Techniques Used: RNA Sequencing, Control, Expressing

a , The number of detected m 6 A sites varies with expression level. Mean m 6 A sites per transcript were quantified for transcripts in each expression bin ( n = 12,034 transcripts, see Extended Data Fig. for n in each bin). Error bars indicate the 95% confidence interval. b , X-chromosomal transcripts harbor fewer m 6 A sites across expression levels. Transcripts from the X chromosome (orange, n = 389 transcripts) compared with the mean of all chromosomes (gray). The numbers of transcripts in expression bins are shown in Extended Data Figure . Significance values for bins 3–8 are indicated by asterisks (autosomes versus X chromosome, two-tailed Wald tests in a generalized linear model for negative binomial data, multiple testing correction; n.s., not significant; * P value < 0.05, ** P value < 0.01). c , The m 6 A content of transcripts from chromosome 11 ( n = 1,031 transcripts) follows the mean of all chromosomes across all expression levels. Transcripts from chromosome 11 (black) compared with the mean of all chromosomes (gray). Analyses for individual chromosomes are shown in Extended Data Figure . d – g , X-chromosomal transcripts have significantly fewer m 6 A sites in male mESCs ( P = 4.1 × 10 –9 , generalized linear model for negative binomial data) ( d ), published m 6 A-seq2 data from mESCs ( e ), mouse heart samples ( P = 8.34 × 10 –11 ) and macrophages ( P value = 1.38 × 10 –8 ) ( f ), and human HEK293T ( P = 0.000203) and C643 cell lines ( P value = 0.001030) ( g ). Mean fold change (log 2 ) of m 6 A sites per transcript on respective chromosomes relative to all chromosomes (Extended Data Fig. ). For mouse data, transcripts of intermediate expression (bins 3–8) are used. For HEK293T data, bins 4–9 were used, and for C643 data, bins 5–10 were used. X-chromosomal and autosomal transcripts are shown in gray and orange, respectively. Chromosomes 11 and X are labeled, for comparison with b and c . P values for comparisons of autosomal versus X-chromosomal transcripts are as in b .

Figure Legend Snippet: a , The number of detected m 6 A sites varies with expression level. Mean m 6 A sites per transcript were quantified for transcripts in each expression bin ( n = 12,034 transcripts, see Extended Data Fig. for n in each bin). Error bars indicate the 95% confidence interval. b , X-chromosomal transcripts harbor fewer m 6 A sites across expression levels. Transcripts from the X chromosome (orange, n = 389 transcripts) compared with the mean of all chromosomes (gray). The numbers of transcripts in expression bins are shown in Extended Data Figure . Significance values for bins 3–8 are indicated by asterisks (autosomes versus X chromosome, two-tailed Wald tests in a generalized linear model for negative binomial data, multiple testing correction; n.s., not significant; * P value < 0.05, ** P value < 0.01). c , The m 6 A content of transcripts from chromosome 11 ( n = 1,031 transcripts) follows the mean of all chromosomes across all expression levels. Transcripts from chromosome 11 (black) compared with the mean of all chromosomes (gray). Analyses for individual chromosomes are shown in Extended Data Figure . d – g , X-chromosomal transcripts have significantly fewer m 6 A sites in male mESCs ( P = 4.1 × 10 –9 , generalized linear model for negative binomial data) ( d ), published m 6 A-seq2 data from mESCs ( e ), mouse heart samples ( P = 8.34 × 10 –11 ) and macrophages ( P value = 1.38 × 10 –8 ) ( f ), and human HEK293T ( P = 0.000203) and C643 cell lines ( P value = 0.001030) ( g ). Mean fold change (log 2 ) of m 6 A sites per transcript on respective chromosomes relative to all chromosomes (Extended Data Fig. ). For mouse data, transcripts of intermediate expression (bins 3–8) are used. For HEK293T data, bins 4–9 were used, and for C643 data, bins 5–10 were used. X-chromosomal and autosomal transcripts are shown in gray and orange, respectively. Chromosomes 11 and X are labeled, for comparison with b and c . P values for comparisons of autosomal versus X-chromosomal transcripts are as in b .

Techniques Used: Expressing, Two Tailed Test, Labeling, Comparison

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Journal: Nature Structural & Molecular Biology

Article Title: RNA stability controlled by m 6 A methylation contributes to X-to-autosome dosage compensation in mammals

doi: 10.1038/s41594-023-00997-7

Figure Lengend Snippet: a , X-chromosomal transcripts are less upregulated upon m 6 A depletion in male mESCs ( P value = 1.86 × 10 –17 , two-tailed Wilcoxon rank-sum test). The cumulative fraction of transcripts (RPKM > 1) on individual autosomes (gray) and the X chromosome (orange) that show a given expression fold change (log 2 , RNA-seq) upon m 6 A depletion (STM2457, 24 h). Mean expression changes for all autosomes are shown as a black line. Effect sizes (blue) show the shift in medians, expressed as percentage of the average interquartile range (IQR) of autosomal and X-chromosomal genes (see ). b , X:A expression ratios show a significant reduction upon m 6 A depletion ( P = 1.4 × 10 –15 , two-tailed t -test of linear contrasts in mixed effect Gaussian model in log scale). c , Differential effects on autosomal and X-chromosomal transcripts already occur after 6 h of m 6 A depletion. Median fold changes (log 2 ) of transcripts from autosomes ( n = 19, gray) and the X chromosome ( n = 1, orange) estimated by RNA-seq at different time points of m 6 A depletion (STM2457, 3, 6, 9 and 12 h). Boxes represent quartiles, center lines denote medians, and whiskers extend to most extreme values within 1.5 × interquartile range. d , Same as a , for human primary fibroblasts (STM2457, 9 h). P value = 6.24 × 10 –6 , two-tailed Wilcoxon rank-sum test. Effect sizes are shown as the shift in medians of the two distributions, expressed as percentage of the average IQR of autosomal and X-chromosomal genes (see ). e , Same as b , for human cell lines ( P value = 0.0000803 (human fibroblasts), P value = 0.0000379 (HEK293T), P value = 0.0003284 (C643), P value = 0.0002982 (RPE1). P values were calculated as in a , with multiple testing correction.

Article Snippet: HEK293T (ATCC, CRL-3216) and C643 (CLS, RRID: CVCL_5969 ) cells were cultured in DMEM (Thermo Fisher Scientific, 21969035) supplemented with 10% fetal bovine serum (FBS, Pan Biotech, P40-47500), 1% P/S (Thermo Fisher Scientific, 10378016), and 1% l -glutamine.

Techniques: Two Tailed Test, Expressing, RNA Sequencing

Journal: Nature Structural & Molecular Biology

Article Title: RNA stability controlled by m 6 A methylation contributes to X-to-autosome dosage compensation in mammals

doi: 10.1038/s41594-023-00997-7

Figure Lengend Snippet: a . Principal component analyses for replicates of RNA-seq experiments under m 6 A-depleted and control conditions for human primary fibroblasts (STM2457, 9 h), HEK293T cells, C643 cells and RPE1 cells (STM2457, 24 h). Replicate number given next to each data point. b . X-chromosomal transcripts show significantly lower fold changes upon m 6 A depletion than autosomal transcripts ( P value = 6.92e-06 [HEK293T, n = 12,856 of autosomal transcripts, n = 443 of X-chromosomal transcripts], P value = 4.53e-05 [C643, n = 11,109 of autosomal transcripts, n = 383 of X-chromosomal transcripts], P value = 0.0001901 [RPE1, n = 10,732 of autosomal transcripts, n = 347 of X-chromosomal transcripts], Wilcoxon rank-sum test). Cumulative fraction of transcripts on individual autosomes (grey) and the X chromosome (orange) that show a given fold change (log 2 ) in m 6 A-depleted (STM2457, 24 h) over control conditions for HEK293T, C643, and RPE1 cells. Mean expression changes for all autosomes are shown as black line. Effect sizes (blue) shown the shift in medians, expressed as percent of the average IQR of autosomal and X-chromosomal genes (see ).

Techniques: RNA Sequencing, Control, Expressing

Journal: Nature Structural & Molecular Biology

Article Title: RNA stability controlled by m 6 A methylation contributes to X-to-autosome dosage compensation in mammals

doi: 10.1038/s41594-023-00997-7

Figure Lengend Snippet: a , The number of detected m 6 A sites varies with expression level. Mean m 6 A sites per transcript were quantified for transcripts in each expression bin ( n = 12,034 transcripts, see Extended Data Fig. for n in each bin). Error bars indicate the 95% confidence interval. b , X-chromosomal transcripts harbor fewer m 6 A sites across expression levels. Transcripts from the X chromosome (orange, n = 389 transcripts) compared with the mean of all chromosomes (gray). The numbers of transcripts in expression bins are shown in Extended Data Figure . Significance values for bins 3–8 are indicated by asterisks (autosomes versus X chromosome, two-tailed Wald tests in a generalized linear model for negative binomial data, multiple testing correction; n.s., not significant; * P value < 0.05, ** P value < 0.01). c , The m 6 A content of transcripts from chromosome 11 ( n = 1,031 transcripts) follows the mean of all chromosomes across all expression levels. Transcripts from chromosome 11 (black) compared with the mean of all chromosomes (gray). Analyses for individual chromosomes are shown in Extended Data Figure . d – g , X-chromosomal transcripts have significantly fewer m 6 A sites in male mESCs ( P = 4.1 × 10 –9 , generalized linear model for negative binomial data) ( d ), published m 6 A-seq2 data from mESCs ( e ), mouse heart samples ( P = 8.34 × 10 –11 ) and macrophages ( P value = 1.38 × 10 –8 ) ( f ), and human HEK293T ( P = 0.000203) and C643 cell lines ( P value = 0.001030) ( g ). Mean fold change (log 2 ) of m 6 A sites per transcript on respective chromosomes relative to all chromosomes (Extended Data Fig. ). For mouse data, transcripts of intermediate expression (bins 3–8) are used. For HEK293T data, bins 4–9 were used, and for C643 data, bins 5–10 were used. X-chromosomal and autosomal transcripts are shown in gray and orange, respectively. Chromosomes 11 and X are labeled, for comparison with b and c . P values for comparisons of autosomal versus X-chromosomal transcripts are as in b .

Techniques: Expressing, Two Tailed Test, Labeling, Comparison