5mc rabbit polyclonal  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc 5mc rabbit polyclonal
    5mc Rabbit Polyclonal, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    5mc rabbit polyclonal  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc 5mc rabbit polyclonal
    5mc Rabbit Polyclonal, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mc d3s2z antibodies  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc mc d3s2z antibodies
    Mc D3s2z Antibodies, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    5mc  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc 5mc
    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA <t>5mC</t> and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.
    5mc, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    5mc - by Bioz Stars, 2023-02
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    Images

    1) Product Images from "A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency"

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    Journal: Cell reports

    doi: 10.1016/j.celrep.2022.110928

    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.
    Figure Legend Snippet: (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.

    Techniques Used: Plasmid Preparation, Labeling, Immunoprecipitation, Co-Immunoprecipitation Assay, Western Blot, Dot Blot, Clone Assay, Tandem Mass Spectroscopy, Two Tailed Test

    KEY RESOURCES TABLE
    Figure Legend Snippet: KEY RESOURCES TABLE

    Techniques Used: Recombinant, Affinity Purification, Mass Spectrometry, Methylated DNA Immunoprecipitation Sequencing, Software

    dna 5mc  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc dna 5mc
    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) <t>DNA</t> <t>5mC</t> and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.
    Dna 5mc, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency"

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    Journal: Cell reports

    doi: 10.1016/j.celrep.2022.110928

    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.
    Figure Legend Snippet: (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.

    Techniques Used: Plasmid Preparation, Labeling, Immunoprecipitation, Co-Immunoprecipitation Assay, Western Blot, Dot Blot, Clone Assay, Tandem Mass Spectroscopy, Two Tailed Test

    KEY RESOURCES TABLE
    Figure Legend Snippet: KEY RESOURCES TABLE

    Techniques Used: Recombinant, Affinity Purification, Mass Spectrometry, Methylated DNA Immunoprecipitation Sequencing, Software

    28692 rrid ab 2798962  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc 28692 rrid ab 2798962
    KEY RESOURCES TABLE
    28692 Rrid Ab 2798962, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/28692 rrid ab 2798962/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    28692 rrid ab 2798962 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency"

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    Journal: Cell reports

    doi: 10.1016/j.celrep.2022.110928

    KEY RESOURCES TABLE
    Figure Legend Snippet: KEY RESOURCES TABLE

    Techniques Used: Recombinant, Affinity Purification, Mass Spectrometry, Methylated DNA Immunoprecipitation Sequencing, Software

    5mc  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc 5mc
    ( A ) Transverse sections of ascending aorta from WT or Eln –/– pups at P0.5 stained for <t>5-methylcytosine</t> <t>(5mC),</t> SMA, and propidium iodide (PI, nuclei). Lu, lumen. Scale bar: 50 μm. ( B ) Histogram representing the percentage of 5mC + SMCs in A ( n = 3 mice). ** P < 0.01 vs. WT by Student’s t test. ( C – E ) haSMCs were pretreated with Scr or siELN and then lysates were analyzed. In C , histogram depicts transcript levels of DNMT1 , DNMT3A , and DNMT3B from qRT-PCR relative to 18S rRNA and normalized to Scr ( n = 6). ** P < 0.01 vs. Scr by Student’s t test. ( D ) Western blots for DNMT1 and GAPDH and densitometry of protein bands in E relative to GAPDH and normalized to Scr ( n = 4). *** P < 0.001 vs. Scr by Student’s t test. ( F and G ) Aortic lysates from WT or Eln –/– mice at P0.5 analyzed by Western blotting for DNMT1 and GAPDH ( F ) with densitometry of protein bands relative to GAPDH and normalized to WT ( G ) ( n = 3 mice). ** P < 0.01 vs. WT by Student’s t test. ( H ) Genomic DNA was isolated from haSMCs pretreated with Scr or siELN and then subjected to methylated DNA chromatin immunoprecipitation (5mC ChIP). Histogram represents 5mC levels at the promoter regions of PSEN1 , PSEN2 , or THS2B (constitutive 5mC positive control) as assessed by qPCR and normalized to Scr ( n = 4). ** P < 0.01, *** P < 0.001 vs. Scr by Student’s t test. All data are averages ± SD.
    5mc, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/5mc/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
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    5mc - by Bioz Stars, 2023-02
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    Images

    1) Product Images from "JAGGED1/NOTCH3 activation promotes aortic hypermuscularization and stenosis in elastin deficiency"

    Article Title: JAGGED1/NOTCH3 activation promotes aortic hypermuscularization and stenosis in elastin deficiency

    Journal: The Journal of Clinical Investigation

    doi: 10.1172/JCI142338

    ( A ) Transverse sections of ascending aorta from WT or Eln –/– pups at P0.5 stained for 5-methylcytosine (5mC), SMA, and propidium iodide (PI, nuclei). Lu, lumen. Scale bar: 50 μm. ( B ) Histogram representing the percentage of 5mC + SMCs in A ( n = 3 mice). ** P < 0.01 vs. WT by Student’s t test. ( C – E ) haSMCs were pretreated with Scr or siELN and then lysates were analyzed. In C , histogram depicts transcript levels of DNMT1 , DNMT3A , and DNMT3B from qRT-PCR relative to 18S rRNA and normalized to Scr ( n = 6). ** P < 0.01 vs. Scr by Student’s t test. ( D ) Western blots for DNMT1 and GAPDH and densitometry of protein bands in E relative to GAPDH and normalized to Scr ( n = 4). *** P < 0.001 vs. Scr by Student’s t test. ( F and G ) Aortic lysates from WT or Eln –/– mice at P0.5 analyzed by Western blotting for DNMT1 and GAPDH ( F ) with densitometry of protein bands relative to GAPDH and normalized to WT ( G ) ( n = 3 mice). ** P < 0.01 vs. WT by Student’s t test. ( H ) Genomic DNA was isolated from haSMCs pretreated with Scr or siELN and then subjected to methylated DNA chromatin immunoprecipitation (5mC ChIP). Histogram represents 5mC levels at the promoter regions of PSEN1 , PSEN2 , or THS2B (constitutive 5mC positive control) as assessed by qPCR and normalized to Scr ( n = 4). ** P < 0.01, *** P < 0.001 vs. Scr by Student’s t test. All data are averages ± SD.
    Figure Legend Snippet: ( A ) Transverse sections of ascending aorta from WT or Eln –/– pups at P0.5 stained for 5-methylcytosine (5mC), SMA, and propidium iodide (PI, nuclei). Lu, lumen. Scale bar: 50 μm. ( B ) Histogram representing the percentage of 5mC + SMCs in A ( n = 3 mice). ** P < 0.01 vs. WT by Student’s t test. ( C – E ) haSMCs were pretreated with Scr or siELN and then lysates were analyzed. In C , histogram depicts transcript levels of DNMT1 , DNMT3A , and DNMT3B from qRT-PCR relative to 18S rRNA and normalized to Scr ( n = 6). ** P < 0.01 vs. Scr by Student’s t test. ( D ) Western blots for DNMT1 and GAPDH and densitometry of protein bands in E relative to GAPDH and normalized to Scr ( n = 4). *** P < 0.001 vs. Scr by Student’s t test. ( F and G ) Aortic lysates from WT or Eln –/– mice at P0.5 analyzed by Western blotting for DNMT1 and GAPDH ( F ) with densitometry of protein bands relative to GAPDH and normalized to WT ( G ) ( n = 3 mice). ** P < 0.01 vs. WT by Student’s t test. ( H ) Genomic DNA was isolated from haSMCs pretreated with Scr or siELN and then subjected to methylated DNA chromatin immunoprecipitation (5mC ChIP). Histogram represents 5mC levels at the promoter regions of PSEN1 , PSEN2 , or THS2B (constitutive 5mC positive control) as assessed by qPCR and normalized to Scr ( n = 4). ** P < 0.01, *** P < 0.001 vs. Scr by Student’s t test. All data are averages ± SD.

    Techniques Used: Staining, Quantitative RT-PCR, Western Blot, Isolation, Methylation, Chromatin Immunoprecipitation, Positive Control

    ( A – C ) haSMCs were treated with Scr or siELN RNA, and then lysates were analyzed. In A , histogram represents ELN and JAG1 transcript levels relative to 18S rRNA as assessed by qRT-PCR and normalized to Scr treatment ( n = 3). Western blots for JAG1 and GAPDH are shown in B , with densitometry of protein bands relative to GAPDH and normalized to Scr in C ( n = 3). * P < 0.05, **** P < 0.0001 vs. Scr by Student’s t test. ( D ) Methylated DNA (5mC) ChIP from haSMCs pretreated with Scr or siELN. Histogram represents 5mC levels at promoter regions of JAG1 or THS2B (positive control) by qPCR and normalized to Scr ( n = 4). ** P < 0.01 vs. Scr by Student’s t test. ( E and F ) Aortic lysates from WT or Eln –/– mice at P0.5 were analyzed by Western blotting for JAG1 and GAPDH (for each blot, 2 aortas were pooled per genotype), with densitometry of JAG1 protein bands relative to GAPDH and normalized to WT ( n = 6 mice). ** P < 0.01 vs. WT by Student’s t test. ( G ) Transverse sections of ascending aorta from WT and Eln –/– mice at P0.5 were stained for JAG1, CD31, SMA, and nuclei (DAPI). n = 3 mice. Lu, lumen. Scale bar: 25 μm. ( H and I ) Protein levels of JAG1 and GAPDH in iPSC-SMCs derived from control or WBS or SVAS patients as assessed by Western blotting with densitometric analysis of JAG1 normalized to GAPDH ( n = 3). *** P < 0.001 by 1-way ANOVA with Tukey’s post hoc test. ( J ) Aortic sections from a WBS male patient (46 years old) and control male (53 years old) stained for JAG1, SMA, and nuclei (PI). Scale bar: 50 μm. ( K ) Column scatter plot represents fluorescence intensity of JAG1 and SMA immunostaining in aortic sections of WBS patients ( n = 5) normalized to age-matched controls ( n = 11). Intensity was quantified on 8 to 10 microscopic fields per patient. ** P < 0.01 vs. control by Student’s t test. All data are averages ± SD.
    Figure Legend Snippet: ( A – C ) haSMCs were treated with Scr or siELN RNA, and then lysates were analyzed. In A , histogram represents ELN and JAG1 transcript levels relative to 18S rRNA as assessed by qRT-PCR and normalized to Scr treatment ( n = 3). Western blots for JAG1 and GAPDH are shown in B , with densitometry of protein bands relative to GAPDH and normalized to Scr in C ( n = 3). * P < 0.05, **** P < 0.0001 vs. Scr by Student’s t test. ( D ) Methylated DNA (5mC) ChIP from haSMCs pretreated with Scr or siELN. Histogram represents 5mC levels at promoter regions of JAG1 or THS2B (positive control) by qPCR and normalized to Scr ( n = 4). ** P < 0.01 vs. Scr by Student’s t test. ( E and F ) Aortic lysates from WT or Eln –/– mice at P0.5 were analyzed by Western blotting for JAG1 and GAPDH (for each blot, 2 aortas were pooled per genotype), with densitometry of JAG1 protein bands relative to GAPDH and normalized to WT ( n = 6 mice). ** P < 0.01 vs. WT by Student’s t test. ( G ) Transverse sections of ascending aorta from WT and Eln –/– mice at P0.5 were stained for JAG1, CD31, SMA, and nuclei (DAPI). n = 3 mice. Lu, lumen. Scale bar: 25 μm. ( H and I ) Protein levels of JAG1 and GAPDH in iPSC-SMCs derived from control or WBS or SVAS patients as assessed by Western blotting with densitometric analysis of JAG1 normalized to GAPDH ( n = 3). *** P < 0.001 by 1-way ANOVA with Tukey’s post hoc test. ( J ) Aortic sections from a WBS male patient (46 years old) and control male (53 years old) stained for JAG1, SMA, and nuclei (PI). Scale bar: 50 μm. ( K ) Column scatter plot represents fluorescence intensity of JAG1 and SMA immunostaining in aortic sections of WBS patients ( n = 5) normalized to age-matched controls ( n = 11). Intensity was quantified on 8 to 10 microscopic fields per patient. ** P < 0.01 vs. control by Student’s t test. All data are averages ± SD.

    Techniques Used: Quantitative RT-PCR, Western Blot, Methylation, Positive Control, Staining, Derivative Assay, Fluorescence, Immunostaining

    anti 5mc  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc anti 5mc
    Characterization of LCSL cells in liver cancer patients. (A) Representative transition regions at the junction of LCSL cells and HCC cells or CCA cells (EpCAM immunostaining) in P2 tumor tissues. Scale bar, 50 μm. (B) Dot plot shows the percentages of Ki-67-positive cells in the four cell types of 50 PLC patients with obvious LCSL cells . Each dot represents the mean value of five randomly selected equal fields of IHC images from one patient. NCT, non-CSC tumor cells. Data are presented as the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed rank test. (C) Representative double immunostaining of EpCAM (red) and 5hmC (dark purple) in one HCC sample with LCSL cells. The green, blue, yellow and red arrowheads indicate PDR, PL, LCSL and HCC cells, respectively. Scale bar, 50 μm. (D) Statistical analysis of <t>5mC,</t> 5hmC and 5fC staining of liver cancer samples. NCT, non-CSC tumor cells. For 5mC and 5hmC, n = 65; for 5fC, n = 34. Data are presented as violin plots with horizontal bars indicating the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed-rank test; ns, not significant.
    Anti 5mc, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti 5mc/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    anti 5mc - by Bioz Stars, 2023-02
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    Images

    1) Product Images from "Spatial Multiomics Analysis Reveals Only Minor Genetic and Epigenetic Changes in Human Liver Cancer Stem-Like Cells Compared With Other Tumor Parenchymal Cells"

    Article Title: Spatial Multiomics Analysis Reveals Only Minor Genetic and Epigenetic Changes in Human Liver Cancer Stem-Like Cells Compared With Other Tumor Parenchymal Cells

    Journal: Frontiers in Cell and Developmental Biology

    doi: 10.3389/fcell.2022.810687

    Characterization of LCSL cells in liver cancer patients. (A) Representative transition regions at the junction of LCSL cells and HCC cells or CCA cells (EpCAM immunostaining) in P2 tumor tissues. Scale bar, 50 μm. (B) Dot plot shows the percentages of Ki-67-positive cells in the four cell types of 50 PLC patients with obvious LCSL cells . Each dot represents the mean value of five randomly selected equal fields of IHC images from one patient. NCT, non-CSC tumor cells. Data are presented as the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed rank test. (C) Representative double immunostaining of EpCAM (red) and 5hmC (dark purple) in one HCC sample with LCSL cells. The green, blue, yellow and red arrowheads indicate PDR, PL, LCSL and HCC cells, respectively. Scale bar, 50 μm. (D) Statistical analysis of 5mC, 5hmC and 5fC staining of liver cancer samples. NCT, non-CSC tumor cells. For 5mC and 5hmC, n = 65; for 5fC, n = 34. Data are presented as violin plots with horizontal bars indicating the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed-rank test; ns, not significant.
    Figure Legend Snippet: Characterization of LCSL cells in liver cancer patients. (A) Representative transition regions at the junction of LCSL cells and HCC cells or CCA cells (EpCAM immunostaining) in P2 tumor tissues. Scale bar, 50 μm. (B) Dot plot shows the percentages of Ki-67-positive cells in the four cell types of 50 PLC patients with obvious LCSL cells . Each dot represents the mean value of five randomly selected equal fields of IHC images from one patient. NCT, non-CSC tumor cells. Data are presented as the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed rank test. (C) Representative double immunostaining of EpCAM (red) and 5hmC (dark purple) in one HCC sample with LCSL cells. The green, blue, yellow and red arrowheads indicate PDR, PL, LCSL and HCC cells, respectively. Scale bar, 50 μm. (D) Statistical analysis of 5mC, 5hmC and 5fC staining of liver cancer samples. NCT, non-CSC tumor cells. For 5mC and 5hmC, n = 65; for 5fC, n = 34. Data are presented as violin plots with horizontal bars indicating the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed-rank test; ns, not significant.

    Techniques Used: Immunostaining, Double Immunostaining, Staining

    An outline of samples used and experiments performed in this study. FFPE and fresh specimens of primary liver cancer patients were collected and screened for LCSL cells by EpCAM IHC staining and tissue/cell morphology. Spatial mutiomics analysis, including in-situ detection of DNA cytosine modifications (5mC, 5hmC and 5fC), WES and WGBS analysis (for P2, P4 and P7 tissues) by CIL-seq, and spatial transcriptomics (for P7 tissues), was performed on those specimens with obvious LCSL cells.
    Figure Legend Snippet: An outline of samples used and experiments performed in this study. FFPE and fresh specimens of primary liver cancer patients were collected and screened for LCSL cells by EpCAM IHC staining and tissue/cell morphology. Spatial mutiomics analysis, including in-situ detection of DNA cytosine modifications (5mC, 5hmC and 5fC), WES and WGBS analysis (for P2, P4 and P7 tissues) by CIL-seq, and spatial transcriptomics (for P7 tissues), was performed on those specimens with obvious LCSL cells.

    Techniques Used: Immunohistochemistry, In Situ

    5mc  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc 5mc
    Effect of GTPs on the expression levels of <t>5mC</t> and 5hmC in UVB-exposed skin and tumors of SKH-1 hairless mice. To define the occurrence of the UVB-induced tumor, the epidermis is demarcated by the dotted white line. The expression of 5mC (red), 5hmC (green), and colocalization (yellow) in the skin ( A ) and tumors ( B ) ( n = 6).
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    Images

    1) Product Images from "Regular Intake of Green Tea Polyphenols Suppresses the Development of Nonmelanoma Skin Cancer through miR-29-Mediated Epigenetic Modifications"

    Article Title: Regular Intake of Green Tea Polyphenols Suppresses the Development of Nonmelanoma Skin Cancer through miR-29-Mediated Epigenetic Modifications

    Journal: Journal of Clinical Medicine

    doi: 10.3390/jcm11020398

    Effect of GTPs on the expression levels of 5mC and 5hmC in UVB-exposed skin and tumors of SKH-1 hairless mice. To define the occurrence of the UVB-induced tumor, the epidermis is demarcated by the dotted white line. The expression of 5mC (red), 5hmC (green), and colocalization (yellow) in the skin ( A ) and tumors ( B ) ( n = 6).
    Figure Legend Snippet: Effect of GTPs on the expression levels of 5mC and 5hmC in UVB-exposed skin and tumors of SKH-1 hairless mice. To define the occurrence of the UVB-induced tumor, the epidermis is demarcated by the dotted white line. The expression of 5mC (red), 5hmC (green), and colocalization (yellow) in the skin ( A ) and tumors ( B ) ( n = 6).

    Techniques Used: Expressing

    An illustration of the mechanism GTPs adopt to prevent photocarcinogenesis via targeting miR-29s-mediated DNA hypermethylation. Exposure to UVB radiation diminishes the expression levels of miR-29s and leads to activation of DNMTs and promotes DNA hypermethylation, resulting in the silencing of tumor suppressor genes and contributing to tumor growth. GTPs treatment blocks the UVB-induced damage and restores the expression of miR-29s to stop DNA hypermethylation through inhibition of DNMTs. As a parallel mechanism, GTPs treatment activates TET enzymes and converts existing 5mC into 5-hmC followed by 5fC and 5caC to promote DNA demethylation, which leads to growth inhibition by reactivation of silenced tumor suppressors. Red arrows indicate the UVB radiation-regulated pathway while green arrows show the GTPs-regulated pathway. DNMT, DNA methyltransferases; TET, ten-eleven-translocation; TDG, thymine DNA glycosylase. Parts of the figure were obtained from Servier Medical Arts, freely available at https://smart.servier.com .
    Figure Legend Snippet: An illustration of the mechanism GTPs adopt to prevent photocarcinogenesis via targeting miR-29s-mediated DNA hypermethylation. Exposure to UVB radiation diminishes the expression levels of miR-29s and leads to activation of DNMTs and promotes DNA hypermethylation, resulting in the silencing of tumor suppressor genes and contributing to tumor growth. GTPs treatment blocks the UVB-induced damage and restores the expression of miR-29s to stop DNA hypermethylation through inhibition of DNMTs. As a parallel mechanism, GTPs treatment activates TET enzymes and converts existing 5mC into 5-hmC followed by 5fC and 5caC to promote DNA demethylation, which leads to growth inhibition by reactivation of silenced tumor suppressors. Red arrows indicate the UVB radiation-regulated pathway while green arrows show the GTPs-regulated pathway. DNMT, DNA methyltransferases; TET, ten-eleven-translocation; TDG, thymine DNA glycosylase. Parts of the figure were obtained from Servier Medical Arts, freely available at https://smart.servier.com .

    Techniques Used: Expressing, Activation Assay, Inhibition, Translocation Assay

    primary antibodies against m5c  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc primary antibodies against m5c
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    5mc  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc 5mc
    Representative images for immunofluorescent (IF) staining of <t>5mC</t> (green) staining ( a ) for blastocyst stage embryos obtained from IV In vivo developed embryos group, Single Single step medium, Seq Sequential medium. Mean ± S.D for the total signal intensity from each pixel of 5mC ( b ). Different letters indicate p < 0.05. DIC Differential Interference Contrast, NC Negative control. Scale bar: 20 µm
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    1) Product Images from "Embryo culture media differentially alter DNA methylating enzymes and global DNA methylation in embryos and oocytes"

    Article Title: Embryo culture media differentially alter DNA methylating enzymes and global DNA methylation in embryos and oocytes

    Journal: Journal of Molecular Histology

    doi: 10.1007/s10735-021-10038-6

    Representative images for immunofluorescent (IF) staining of 5mC (green) staining ( a ) for blastocyst stage embryos obtained from IV In vivo developed embryos group, Single Single step medium, Seq Sequential medium. Mean ± S.D for the total signal intensity from each pixel of 5mC ( b ). Different letters indicate p < 0.05. DIC Differential Interference Contrast, NC Negative control. Scale bar: 20 µm
    Figure Legend Snippet: Representative images for immunofluorescent (IF) staining of 5mC (green) staining ( a ) for blastocyst stage embryos obtained from IV In vivo developed embryos group, Single Single step medium, Seq Sequential medium. Mean ± S.D for the total signal intensity from each pixel of 5mC ( b ). Different letters indicate p < 0.05. DIC Differential Interference Contrast, NC Negative control. Scale bar: 20 µm

    Techniques Used: Staining, In Vivo, Negative Control

    Representative images for immunofluorescent (IF) staining of 5mC (green) staining ( a ) for MII stage oocytes obtained from In vivo /Vas In vivo matured MII stage oocytes obtained from female mice mated with vasectomised males, In Vivo /HS In vivo matured MII stage oocytes obtained from Hormonally Stimulated female mice, Single Single step medium, Seq Sequential medium. Mean ± S.D for the total signal intensity from each pixel of 5mC ( b ). Different letters indicate p < 0.05. DIC Differential Interference Contrast, NC Negative control. Scale bar: 10 µm
    Figure Legend Snippet: Representative images for immunofluorescent (IF) staining of 5mC (green) staining ( a ) for MII stage oocytes obtained from In vivo /Vas In vivo matured MII stage oocytes obtained from female mice mated with vasectomised males, In Vivo /HS In vivo matured MII stage oocytes obtained from Hormonally Stimulated female mice, Single Single step medium, Seq Sequential medium. Mean ± S.D for the total signal intensity from each pixel of 5mC ( b ). Different letters indicate p < 0.05. DIC Differential Interference Contrast, NC Negative control. Scale bar: 10 µm

    Techniques Used: Staining, In Vivo, Negative Control

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    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA <t>5mC</t> and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.
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    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) <t>DNA</t> <t>5mC</t> and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.
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    Characterization of LCSL cells in liver cancer patients. (A) Representative transition regions at the junction of LCSL cells and HCC cells or CCA cells (EpCAM immunostaining) in P2 tumor tissues. Scale bar, 50 μm. (B) Dot plot shows the percentages of Ki-67-positive cells in the four cell types of 50 PLC patients with obvious LCSL cells . Each dot represents the mean value of five randomly selected equal fields of IHC images from one patient. NCT, non-CSC tumor cells. Data are presented as the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed rank test. (C) Representative double immunostaining of EpCAM (red) and 5hmC (dark purple) in one HCC sample with LCSL cells. The green, blue, yellow and red arrowheads indicate PDR, PL, LCSL and HCC cells, respectively. Scale bar, 50 μm. (D) Statistical analysis of <t>5mC,</t> 5hmC and 5fC staining of liver cancer samples. NCT, non-CSC tumor cells. For 5mC and 5hmC, n = 65; for 5fC, n = 34. Data are presented as violin plots with horizontal bars indicating the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed-rank test; ns, not significant.
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    Characterization of LCSL cells in liver cancer patients. (A) Representative transition regions at the junction of LCSL cells and HCC cells or CCA cells (EpCAM immunostaining) in P2 tumor tissues. Scale bar, 50 μm. (B) Dot plot shows the percentages of Ki-67-positive cells in the four cell types of 50 PLC patients with obvious LCSL cells . Each dot represents the mean value of five randomly selected equal fields of IHC images from one patient. NCT, non-CSC tumor cells. Data are presented as the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed rank test. (C) Representative double immunostaining of EpCAM (red) and 5hmC (dark purple) in one HCC sample with LCSL cells. The green, blue, yellow and red arrowheads indicate PDR, PL, LCSL and HCC cells, respectively. Scale bar, 50 μm. (D) Statistical analysis of <t>5mC,</t> 5hmC and 5fC staining of liver cancer samples. NCT, non-CSC tumor cells. For 5mC and 5hmC, n = 65; for 5fC, n = 34. Data are presented as violin plots with horizontal bars indicating the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed-rank test; ns, not significant.
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    Image Search Results


    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.

    Journal: Cell reports

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    doi: 10.1016/j.celrep.2022.110928

    Figure Lengend Snippet: (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.

    Article Snippet: The membrane was dried, auto-crosslinked with 1200 × 100 μJ/cm 2 , and blocked with 5% milk/TBST for 1 h. Next, the membrane was incubated with 5mC (Cell Signaling, 28692) or 5hmC (Active Motif, 39769) antibodies, the same as the Western blot analysis.

    Techniques: Plasmid Preparation, Labeling, Immunoprecipitation, Co-Immunoprecipitation Assay, Western Blot, Dot Blot, Clone Assay, Tandem Mass Spectroscopy, Two Tailed Test

    KEY RESOURCES TABLE

    Journal: Cell reports

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    doi: 10.1016/j.celrep.2022.110928

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: The membrane was dried, auto-crosslinked with 1200 × 100 μJ/cm 2 , and blocked with 5% milk/TBST for 1 h. Next, the membrane was incubated with 5mC (Cell Signaling, 28692) or 5hmC (Active Motif, 39769) antibodies, the same as the Western blot analysis.

    Techniques: Recombinant, Affinity Purification, Mass Spectrometry, Methylated DNA Immunoprecipitation Sequencing, Software

    (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.

    Journal: Cell reports

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    doi: 10.1016/j.celrep.2022.110928

    Figure Lengend Snippet: (A) Protein ratios of FLAG-IP (TET1)versus Control-IP (empty vector) AP-MS in two replicates with reciprocal SILAC labeling are plotted, and a few proteins in the TET1 interactome are indicated. (B and F) Co-immunoprecipitation (co-IP) of TET1 partners (B) or TET1/2 (F) by FLAG-IP followed by Western blot analysis in ESCs. (C and D) Co-IP by endogenous PSPC1 (C) and TET1 (D) antibodies followed by western blot analysis in ESCs. (E) Western blot analysis in Tet1/2/3 triple-KO ( Tet TKO) ESCs rescued with FLAG-tagged TET1 or TET2 in ESCs. (G) DNA 5mC and 5hmC dot-blot analysis of WT and Pspc1 KO (two independent clones, C4 and C9) ESCs. dsDNA antibody is reblotted as the loading control. Dnmt1/3a/3b triple-KO ( Dnmt TKO) and Tet TKO ESCs serve as negative controls of 5mC and 5hmC, respectively. (H) UHPLC-MS/MS quantification of 5′-methyl-deoxycytidine (5mC) and 5′-hydroxymethyl-deoxycytidine (5hmC) over deoxycytidine (dC) from genomic DNA of WT and Pspc1 KO ESCs. Experiments were performed in biological duplicates with technical triplicates; p value is from two-tailed t test, and “n.s.” denotes statistically non-significant.

    Article Snippet: DNA 5mC , Cell Signaling , Cat. 28692; RRID: AB_2798962.

    Techniques: Plasmid Preparation, Labeling, Immunoprecipitation, Co-Immunoprecipitation Assay, Western Blot, Dot Blot, Clone Assay, Tandem Mass Spectroscopy, Two Tailed Test

    KEY RESOURCES TABLE

    Journal: Cell reports

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    doi: 10.1016/j.celrep.2022.110928

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: DNA 5mC , Cell Signaling , Cat. 28692; RRID: AB_2798962.

    Techniques: Recombinant, Affinity Purification, Mass Spectrometry, Methylated DNA Immunoprecipitation Sequencing, Software

    KEY RESOURCES TABLE

    Journal: Cell reports

    Article Title: A TET1-PSPC1- Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

    doi: 10.1016/j.celrep.2022.110928

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: DNA 5mC , Cell Signaling , Cat. 28692; RRID: AB_2798962.

    Techniques: Recombinant, Affinity Purification, Mass Spectrometry, Methylated DNA Immunoprecipitation Sequencing, Software

    Characterization of LCSL cells in liver cancer patients. (A) Representative transition regions at the junction of LCSL cells and HCC cells or CCA cells (EpCAM immunostaining) in P2 tumor tissues. Scale bar, 50 μm. (B) Dot plot shows the percentages of Ki-67-positive cells in the four cell types of 50 PLC patients with obvious LCSL cells . Each dot represents the mean value of five randomly selected equal fields of IHC images from one patient. NCT, non-CSC tumor cells. Data are presented as the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed rank test. (C) Representative double immunostaining of EpCAM (red) and 5hmC (dark purple) in one HCC sample with LCSL cells. The green, blue, yellow and red arrowheads indicate PDR, PL, LCSL and HCC cells, respectively. Scale bar, 50 μm. (D) Statistical analysis of 5mC, 5hmC and 5fC staining of liver cancer samples. NCT, non-CSC tumor cells. For 5mC and 5hmC, n = 65; for 5fC, n = 34. Data are presented as violin plots with horizontal bars indicating the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed-rank test; ns, not significant.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Spatial Multiomics Analysis Reveals Only Minor Genetic and Epigenetic Changes in Human Liver Cancer Stem-Like Cells Compared With Other Tumor Parenchymal Cells

    doi: 10.3389/fcell.2022.810687

    Figure Lengend Snippet: Characterization of LCSL cells in liver cancer patients. (A) Representative transition regions at the junction of LCSL cells and HCC cells or CCA cells (EpCAM immunostaining) in P2 tumor tissues. Scale bar, 50 μm. (B) Dot plot shows the percentages of Ki-67-positive cells in the four cell types of 50 PLC patients with obvious LCSL cells . Each dot represents the mean value of five randomly selected equal fields of IHC images from one patient. NCT, non-CSC tumor cells. Data are presented as the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed rank test. (C) Representative double immunostaining of EpCAM (red) and 5hmC (dark purple) in one HCC sample with LCSL cells. The green, blue, yellow and red arrowheads indicate PDR, PL, LCSL and HCC cells, respectively. Scale bar, 50 μm. (D) Statistical analysis of 5mC, 5hmC and 5fC staining of liver cancer samples. NCT, non-CSC tumor cells. For 5mC and 5hmC, n = 65; for 5fC, n = 34. Data are presented as violin plots with horizontal bars indicating the mean ± SD. ***, p < 0.001 by Wilcoxon matched-pairs signed-rank test; ns, not significant.

    Article Snippet: The primary antibodies used were as follows: anti-5mC (1:5000, Cat#: 28692; Cell Signaling Technology), anti-5hmC (1:10000, Cat#: 39769; Active Motif); and anti-5fC (1:1000, Cat#: 61227; Active Motif).

    Techniques: Immunostaining, Double Immunostaining, Staining

    An outline of samples used and experiments performed in this study. FFPE and fresh specimens of primary liver cancer patients were collected and screened for LCSL cells by EpCAM IHC staining and tissue/cell morphology. Spatial mutiomics analysis, including in-situ detection of DNA cytosine modifications (5mC, 5hmC and 5fC), WES and WGBS analysis (for P2, P4 and P7 tissues) by CIL-seq, and spatial transcriptomics (for P7 tissues), was performed on those specimens with obvious LCSL cells.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Spatial Multiomics Analysis Reveals Only Minor Genetic and Epigenetic Changes in Human Liver Cancer Stem-Like Cells Compared With Other Tumor Parenchymal Cells

    doi: 10.3389/fcell.2022.810687

    Figure Lengend Snippet: An outline of samples used and experiments performed in this study. FFPE and fresh specimens of primary liver cancer patients were collected and screened for LCSL cells by EpCAM IHC staining and tissue/cell morphology. Spatial mutiomics analysis, including in-situ detection of DNA cytosine modifications (5mC, 5hmC and 5fC), WES and WGBS analysis (for P2, P4 and P7 tissues) by CIL-seq, and spatial transcriptomics (for P7 tissues), was performed on those specimens with obvious LCSL cells.

    Article Snippet: The primary antibodies used were as follows: anti-5mC (1:5000, Cat#: 28692; Cell Signaling Technology), anti-5hmC (1:10000, Cat#: 39769; Active Motif); and anti-5fC (1:1000, Cat#: 61227; Active Motif).

    Techniques: Immunohistochemistry, In Situ