Journal: Nature Communications

Article Title: D-2-hydroxyglutarate impairs DNA repair through epigenetic reprogramming

doi: 10.1038/s41467-025-56781-2

Figure Lengend Snippet: a 5hmC Dot blot assay. Cells were treated with 150 μM TMZ, 0.5 mM D-2-HG, 10 mM αKG, TET1 or TET2 overexpression for 24 h, 400, 200, 100, 50, 25, 12.5 ng gDNA was used for the assay. 5hmC was monitored with the antibodies. b MeDIP assay. DRGFP U2OS cells were treated with 0.5 μM Shield1 and 0.2 mM TA for 2 h. * p < 0.05, ** p < 0.01. ns: non-significant. For −1500 to 1000 locus, Sce-I+ vs D-2-HG, D-2-HG vs D-2-HG + αKG, all p < 0.0001; −1500, D-2-HG vs D-2-HG + TET1/TET2, p < 0.0001; −500, D-2-HG vs D-2-HG + TET1, p = 0.0423; D-2-HG vs D-2-HG + TET2, p = 0.0230; −180, D-2-HG vs D-2-HG + TET1, p = 0.0014; D-2-HG vs D-2-HG + TET2, p = 0.0006; 150, D-2-HG vs D-2-HG + TET1, p = 0.0010; D-2-HG vs D-2-HG + TET2, p = 0.0034; 500, D-2-HG vs D-2-HG + TET1, p = 0.0060; D-2-HG vs D-2-HG + TET2, p = 0.0156; 1000, D-2-HG vs D-2-HG + TET1, p = 0.0024; D-2-HG vs D-2-HG + TET2, p = 0.0096; group differences were tested with one-way ANOVA. Data are mean ± SEM from three independent experiments. c , d Laser micro-irradiation. Scale bar: 5 μm. e , f Quantification of data shown in ( c ) and ( d ). Over 60 cells were obtained from 5–7 imaging views ( e , DMSO, n = 5; D-2-HG, n = 5, D-2-HG + αKG, n = 6, D-2-HG + TET1, n = 8, D-2-HG + TET2, n = 7; f DMSO, n = 6; D-2-HG, n = 5, D-2-HG + αKG, n = 5, D-2-HG + TET1, n = 7, D-2-HG + TET2, n = 6). * p < 0.05, ** p < 0.01. e All indicated p < 0.0001; f DMSO vs D-2-HG, p < 0.0001; D-2-HG vs D-2-HG + αKG, p < 0.0001; D-2-HG vs D-2-HG + TET1, p = 0.0069; D-2-HG vs D-2-HG + TET2, p = 0.0277; group differences were tested with one-way ANOVA. Data are mean ± SEM from three independent experiments. g ChIP-qPCR assay. DRGFP U2OS cells were treated with 0.5 μM Shield1 and 0.2 mM TA for 0.5, 1, 2, 4, 6, 12, or 24 h. Two genomic regions −180 bp and +150 bp adjacent of DSB sites were monitored. h ChIP-qPCR assay targeting FRA7D, FRA7-2, and FRA21. Data are presented as mean ± SEM from three independent experiments. Source Data are provided as a Source Data file.

Article Snippet: The primary antibodies including CTCF (Abcam, ab70303), γH2A.X (Millipore, 05-636), RAD51 (Abcam, ab88572), BRCA2 (Bethyl Laboratories, A303-434A), 5hmC (Active motif, 39069), TET1 (GeneTex, GTX124207), TET2 (Thermo Fisher, PA5-78514), RPA70/RPA1 (Cell Signaling Technology, 2198), or 53BP1 (Novus Biological, NB100-304) were used at 1:1000 dilution.

Techniques: Dot Blot, Over Expression, Methylated DNA Immunoprecipitation, Irradiation, Imaging, ChIP-qPCR

Journal: Cell Death & Disease

Article Title: Understanding the function of Pax5 in development of docetaxel-resistant neuroendocrine-like prostate cancers

doi: 10.1038/s41419-024-06916-y

Figure Lengend Snippet: A ATAC-seq and H3K18/H3K27 acetylation ChIP-seq signal near the Pax5 promoter of C4-2B and C4-2BER cells. B Expression of Pbx1 in DKD vs C4-2 and in C4-2BER vs C4-2B. ** p < 0.001 by Student’s t test. Error bars represent the standard deviation between N = 3 biological replicates. C Immunoblots for Pbx1 expression in adeno and NE-like cells. HSC70 represents the loading control. Immunoblots are representative of N = 3 independent experiments. D , E RT-PCR represent the Pax5 expression following the depletion of Pbx1 in the DKD and C4-2BER cells, respectively. ** P < 0.001 and * P < 0.01 through Student’s t test. Error bars represent standard errors between N = 3 biological replicates. F Immunoblot for the Pax5 expression following Pbx1 depletion in C4-2BER cells. HSC70 is the loading control. G Pbx1 ChIP-qPCR was carried out using the primers designed upstream of TSS of Pax5. –ve sign represents downstream of Pax5 promoter TSS. Number represents the position near which Pax5 primers have been developed. Pbx1 binding at Pax5 promoter was compared in adeno and NE-like state. Enrichment of Pbx1 binding was calculated with respect to IgG control after normalization of inputs. ** P < 0.001 and * P < 0.01 by Student’s t test. Error bars represent standard deviation between N = 3 biological replicates. H Schematic of Epic methylation array analysis of Pax5 gene in DKD and C4-2 cells. Green triangles represent the region that falls under the CpG island. Cytosine methylation status at the proximal promoter of both the cell lines was magnified and sequence has been shown to indicate the methylation status in each region. Red represents methylated/modified cytosine whereas green is demethylated cytosine. Pbx1 binding sight at the promoter is represented by arrow. I Immunoblot for TET2 expression in various prostate cancer cell lines. HSP70 functions as loading control. J 5hmC footprint mark was analyzed by ChIP-qPCR at Pbx1 binding site of Pax5 promoter region. Fold enrichment of 5 hmC footprint as well as Pbx1 binding was calculated with respect to IgG control after normalization of inputs. * P < 0.01 and ** P < 0.001 by Student’s t test. Error bars represent standard deviation between biological replicates. K 5hmC and Pbx1 ChIP-qPCR was carried out following the treatment of DKD cells with Bobcat339 (50 μM for 18–24 h) and compared with control untreated sample. Primer 1 (Pbx1 binding site for Pax5) was used here to amplify the ChIP-enriched region. * P < 0.01 and ** P < 0.001 by Student’s t test. Error bars represent standard deviation between N = 3 biological replicates. Fold enrichment of 5hmC footprint as well as Pbx1 binding was calculated with respect to IgG control after normalization of inputs. L RT-PCR was carried out to analyze the Pax5 gene expression following treatment of DKD cells with 5-Azacytidine (0.1 μM for 5–7 days) and Bobcat339. M Schematic representing the overall Pbx1/Pax5 regulation in t-NEPC maintenance.

Article Snippet: 5hmC (Rabbit) , Active Motif, #39069.

Techniques: ChIP-sequencing, Expressing, Standard Deviation, Western Blot, Control, Reverse Transcription Polymerase Chain Reaction, ChIP-qPCR, Binding Assay, Methylation, Sequencing, Modification, Gene Expression

Journal: Cell Death & Disease

Article Title: Understanding the function of Pax5 in development of docetaxel-resistant neuroendocrine-like prostate cancers

doi: 10.1038/s41419-024-06916-y

Figure Lengend Snippet:

Article Snippet: 5hmC (Rabbit) , Active Motif, #39069.

Techniques:

Journal: Cell Death & Disease

Article Title: Understanding the function of Pax5 in development of docetaxel-resistant neuroendocrine-like prostate cancers

doi: 10.1038/s41419-024-06916-y

Figure Lengend Snippet:

Article Snippet: 5hmC (Rabbit) , Active Motif, #39069.

Techniques:

Journal: Nature Communications

Article Title: Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

doi: 10.1038/s41467-024-50725-y

Figure Lengend Snippet: A Schematic of experimental procedure and tissues used to profile global levels of 5mC and 5hmC by DNA mass spectrometry (nLC-MS/MS). Data are presented as mean ± SEM; statistical significance was assessed using two-sided unpaired Welch’s t -test with Holm-Šídák correction for multiple comparisons. B Dot blot for 5hmC using increasing amounts of gDNA isolated from young and old ( n = 4 each) mouse livers; + control is 200 ng of young mouse hippocampus gDNA, – control is water. Signal quantifications are shown on the right. Data are presented as mean ± SD; statistical significance was assessed using two-way ANOVA with Šídák correction for multiple comparisons. AU represents arbitrary fluorescence units. C Representative immunofluorescence microscopy for 5hmC in young and old ( n = 2 each) sex-matched liver sections. The mean 5hmC signal intensity per nucleus is quantified on the right, using data from 10 fields of view for each of the two young and two old biological replicates. Horizontal bar represents median; statistical significance was assessed using two-sided unpaired Welch’s t -test. Source data are provided as a Source Data file. Illustration credit: Endosymbiont GmbH.

Article Snippet: The membrane was then blocked in 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 1 h at room temperature followed by incubation with 1:10,000 dilution of 5hmC antibody (Active Motif, 39069) overnight at 4 °C.

Techniques: Mass Spectrometry, Tandem Mass Spectroscopy, Dot Blot, Isolation, Control, Fluorescence, Immunofluorescence, Microscopy

Journal: Nature Communications

Article Title: Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

doi: 10.1038/s41467-024-50725-y

Figure Lengend Snippet: A Principal component analysis (PCA) plot using input subtracted 5hmC bigWig files of young and old ( n = 4 each) mice liver. B Volcano plot of differentially hydroxymethylated regions (DHMRs) between old and young ( n = 4 each) mouse liver; identified by QSEA with an FDR < 0.05. Hypo DHMRs (FC ≤ −2) are regions with less enrichment in the old and hyper DHMRs (FC ≥ 2) are regions with higher enrichment in the old. C Metaplots of young and old ( n = 4 each) mouse liver 5hmC signal at the DHMRs identified by QSEA. D Example genome browser tracks for mouse liver hyper DHMRs ( Ppig and an intergenic region) and hypo DHMRs ( Rbm47 and Car5a ). E Gene ontology (GO) terms associated with the DHMRs from ( B ) using GREAT. The top 5 biological process terms with FDR < 0.05 are shown. F Pie charts showing CpG and genic/intergenic annotations of the DHMRs from ( B ). G Metaplots of young and old ( n = 4 each) mouse liver 5hmC signal over the gene bodies of all mm10 genes; signal quantifications are shown on the side. Statistical significance was assessed using two-sided unpaired Welch’s t -test. For the box plot, the horizontal line within each box represents the 50th, while the bounds of the box depict the 25th and 75th percentile of the data. The whiskers extend to the minima (the smallest value within 1.5 times the interquartile range (IQR) below the first quartile, excluding outliers) and the maxima (the largest value within 1.5 times the IQR above the third quartile, excluding outliers). Source data are provided as a Source Data file.

Article Snippet: The membrane was then blocked in 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 1 h at room temperature followed by incubation with 1:10,000 dilution of 5hmC antibody (Active Motif, 39069) overnight at 4 °C.

Techniques:

Journal: Nature Communications

Article Title: Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

doi: 10.1038/s41467-024-50725-y

Figure Lengend Snippet: A Metaplots of merged young and old ( n = 4 each) mouse liver 5hmC signal over gene bodies with low ( n = 6,340), intermediate ( n = 6,339), and high ( n = 6,339) average mRNA counts for young (left) and old (right) samples ( n = 3 each). B Correlation between average gene body 5hmC signal (100 ranked groups) and variance in mRNA FC (old vs young) among the genes per group for young (left) and old (right). ρ = Spearman’s correlation coefficient, p -values were derived from Spearman’s rank correlation. C Box plots showing mRNA FC of old vs young ( n = 3 each) for genes downregulated or upregulated with age. D Metaplots of young and old ( n = 4 each) mouse liver 5hmC signal over gene bodies in ( C ). Quantifications are depicted below the plot; statistical significance was assessed using two-sided unpaired Welch’s t -test. E Same as ( C ) except for genes with minimal or maximal expression change between old and young ( n = 3 each). F Metaplots of young and old ( n = 4 each) mouse liver 5hmC signal over gene bodies in ( E ). Quantifications are depicted below the plot; statistical significance was assessed using two-sided unpaired Welch’s t -test. G Metaplots of young and old ( n = 4 each) mouse liver 5mC signal over gene bodies in ( E ) with minimal (left) and maximal (right) expression change with age. Quantifications are depicted below the plot; statistical significance was assessed using two-sided unpaired Welch’s t -test. H Box plots showing the distribution of various genic features for the genes with minimal and maximal expression changes between old vs young ( n = 3 each) mice. Statistical significance was assessed using two-sided unpaired Welch’s t -test. For all box plots ( C – H ), the horizontal line within each box represents the 50th, while the bounds of the box depict the 25th and 75th percentile of the data. The whiskers extend to the minima (the smallest value within 1.5 times the IQR below the first quartile, excluding outliers) and the maxima (the largest value within 1.5 times the IQR above the third quartile, excluding outliers). Source data are provided as a Source Data file.

Article Snippet: The membrane was then blocked in 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 1 h at room temperature followed by incubation with 1:10,000 dilution of 5hmC antibody (Active Motif, 39069) overnight at 4 °C.

Techniques: Derivative Assay, Expressing

Journal: Nature Communications

Article Title: Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

doi: 10.1038/s41467-024-50725-y

Figure Lengend Snippet: A Schematic for 70% partial hepatectomy. B Relative global 5hmC signal for young and old ( n = 3 each) mouse liver samples at the indicated times. Data are presented as mean ± SD. Statistical significance was assessed using two-way ANOVA with Geisser-Greenhouse correction. C Metaplot of 5hmC signal over bodies of all mm10 genes for indicated groups. Quantifications are shown on the side. D Metaplot of 5hmC signal across genes bodies with minimal (left) and maximal (right) expression changes between old pre-surgery vs young pre-surgery ( n = 3 each) mRNA comparisons. Quantifications are shown below. For ( C - D ), statistical significance was assessed using one-way ANOVA with Tukey’s multiple comparisons post-hoc test. E Box plots showing transcriptional changes for “genes with minimal change with age” (from D , left). Statistical significance was assessed using Mann–Whitney U test. F Box plots showing transcriptional changes for indicated group comparisons. Statistical significance was assessed using a Mann–Whitney U test with FDR correction (Benjamini-Hochberg). G Schematic showing vitamin C treatment in T24 bladder cancer cells from Peng et al. . H Metaplot of 5hmC signal over the bodies of all hg19 genes in vitamin C-treated T24 cells and untreated controls ( n = 1 each). I Box plots showing absolute mRNA FC distribution of genes with minimal and maximal expression changes in vitamin C-treated T24 cells vs untreated controls ( n = 2 independent cell cultures) . Below, metaplot of 5hmC signal across gene bodies with minimal (left) and maximal (right) expression changes. J Box plots showing transcriptional changes for all genes in vitamin C-treated T24 cells vs untreated controls ( n = 2 independent cell cultures per group). Statistical significance was assessed using one-way ANOVA. For all box plots, the horizontal line within each box represents the 50th, while the bounds of the box depict the 25th and 75th percentile of the data. The whiskers extend to the minima (the smallest value within 1.5 times the IQR below the first quartile, excluding outliers) and the maxima (the largest value within 1.5 times the IQR above the third quartile, excluding outliers). Source data are provided as a Source Data file. Illustration credit: Endosymbiont GmbH.

Article Snippet: The membrane was then blocked in 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 1 h at room temperature followed by incubation with 1:10,000 dilution of 5hmC antibody (Active Motif, 39069) overnight at 4 °C.

Techniques: Expressing, MANN-WHITNEY

Journal: Nature Communications

Article Title: Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

doi: 10.1038/s41467-024-50725-y

Figure Lengend Snippet: A Schematic of oligo mass-spec experimental procedure. B Volcano plot showing differentially enriched proteins in old mice for the 5hmC oligo 1 pull-down vs input ( n = 4 each). Some significantly enriched or de-enriched interactors are labeled. C Same as ( B ) except for the 5hmC oligo 2 pull-down vs input ( n = 4 each) in the old. D GO terms associated with proteins depleted/de-enriched or enriched for oligo 1 in the old 5hmC vs young C and mC ( n = 4 each) comparison. E GO terms associated with proteins depleted/de-enriched or enriched for oligo 2 in the old 5hmC vs old C and mC ( n = 4 each) comparison (top) and the old 5hmC vs young C and mC ( n = 4 each) comparison (bottom). F Number of differential splicing events detected in RNA-seq data between old and young ( n = 3 each) samples at p < 0.05 using rMATS (top). Number of events and the unique number of genes are indicated. Number of differential splicing events grouped by increasing gene body 5hmC signal in old (middle). Number of differential splicing events grouped by minimal or maximal expression change with age (bottom). G Bar plots showing differential isoform usage from dRNA-seq results with young and old ( n = 4 each) samples for genes with minimal and maximal expression changes with age at indicated p -value thresholds derived from the rMATS statistical model ( H ) Transcript length (top) and poly A length (bottom) distribution for genes that undergo minimal or maximal expression changes between old and young ( n = 4 each); statistical significance was assessed using Mann–Whitney U test. For (B-E), statistical differences for each protein were assessed using Welch’s t -test (if the F -test p -value was <0.05); otherwise, the standard Student’s t -test was used. Source data are provided as a Source Data file. Illustration credit: Endosymbiont GmbH.

Article Snippet: The membrane was then blocked in 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 1 h at room temperature followed by incubation with 1:10,000 dilution of 5hmC antibody (Active Motif, 39069) overnight at 4 °C.

Techniques: Mass Spectrometry, Labeling, Comparison, RNA Sequencing, Expressing, Derivative Assay, MANN-WHITNEY

Journal: Nature Communications

Article Title: Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

doi: 10.1038/s41467-024-50725-y

Figure Lengend Snippet: A Normalized mRNA counts in young and old ( n = 3 each) mouse liver for 5hmC-relevant enzymes. Data are presented as mean ± SEM; statistical significance was assessed using multiple two-sided unpaired t -test with FDR correction (Benjamini, Krieger, and Yekutieli). B TET activity assay in young and old ( n = 4 each) mouse liver lysates. C Dot blot for 5hmC signal using gDNA isolated from proliferating and contact inhibition-induced quiescent HepG2 cells ( n = 3 independent cell cultures sourced from the same vial). + control is 200 ng of young mouse hippocampus gDNA, – control is water. Quantifications are depicted below. D ATP production assay using proliferating and contact-inhibited quiescent HepG2 cells ( n = 3 technical replicates for each of 3 independent cell cultures sourced from the same vial). E TMRM mitoprobe assay with proliferating and contact-inhibited quiescent HepG2 cells ( n = 3 independent cell cultures sourced from the same vial). F Dot blot of 5hmC using gDNA isolated from proliferating and IRIS, ETIS, and OSIS WI-38 cells ( n = 3 independent cell cultures sourced from a single vial). +control is 50 ng of young mouse hippocampus gDNA, – control is water. Quantifications are shown below. G Dot blot for 5hmC using gDNA isolated from HepG2 cells treated with vitamin C ( n = 2 independent cell cultures sourced from a single vial). + control is 200 ng of young mouse hippocampus gDNA, – control is water. Quantifications are depicted below. H ATP production assay using proliferating and vitamin C treated HepG2 cells ( n = 3 technical replicates for each of 3 independent cell cultures sourced from the same vial). I TMRM mitoprobe assay with proliferating and vitamin C treated HepG2 cells ( n = 3 independent cell cultures sourced from the same vial); statistical significance was assessed using two-sided unpaired Welch’s t -test. For panels ( B – I ), data are presented as mean ± SD. Statistical significance was assessed using two-sided unpaired Welch’s t -test, except for dot blots ( C , F , G ), which used two-way ANOVA with Tukey’s multiple comparisons post-hoc test. AU represents arbitrary fluorescence units. Source data are provided as a Source Data file.

Article Snippet: The membrane was then blocked in 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 1 h at room temperature followed by incubation with 1:10,000 dilution of 5hmC antibody (Active Motif, 39069) overnight at 4 °C.

Techniques: Activity Assay, Dot Blot, Isolation, Inhibition, Control, Fluorescence

Journal: Nature Communications

Article Title: Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

doi: 10.1038/s41467-024-50725-y

Figure Lengend Snippet: A Schematic outline of procedure, age groups, and tissues chosen from the GTEx project. B Metaplots of 5hmC signal from He et al. over gene bodies of brain-differential and brain-specific genes, C heart-differential and heart-specific genes, and ( D ) liver-differential and liver-specific genes; statistical significance was assessed using Mann–Whitney U test. E Metaplots of 5hmC signal from Cui et al. over gene bodies of brain-differential and brain-specific genes, ( F ) heart-differential and heart-specific genes, and ( G ) liver-differential and liver-specific genes; statistical significance was assessed using Mann–Whitney U test. H Model illustrating the transcriptionally restrictive role of 5hmC and its propensity to downregulate tissue-specific functions with increasing age. Source data are provided as a Source Data file. Illustration credit: Endosymbiont GmbH.

Article Snippet: The membrane was then blocked in 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 1 h at room temperature followed by incubation with 1:10,000 dilution of 5hmC antibody (Active Motif, 39069) overnight at 4 °C.

Techniques: MANN-WHITNEY

Journal: Nature

Article Title: In vitro reconstitution of epigenetic reprogramming in the human germ line

doi: 10.1038/s41586-024-07526-6

Figure Lengend Snippet: a , Scheme of the human TET1 locus, with the illustration of PAM (protospacer adjacent motif) and guide RNA sequences in the exon 6. Black boxes indicate the exons. b , Sequences of the targeted loci in two TET1 knockout (KO) cell lines [ TET1 KO#1 and # 2 (M1- BTAG TET1 −/− #142 and #2725)]. c , Dot-blot analysis of genomic 5hmC levels in wild-type and TET1 KO hiPSCs (1 replicate for each line). d , Karyotype of TET1 KO#1 and #2 hiPSCs (top: chromosome spreads; bottom: percentage of cells with 46 or other chromosome numbers) (1 biological replicate for each line). Bar, 10 μm. e , Mass spectrometric analysis [log 2 (signal intensities)] for TET1 and its truncated protein potentially derived from the TET1 KO allele in wild-type and TET1 KO cells. Peptides from the full-length (top), but not the truncated (bottom), TET1 were detected from the wild-type cells (red and blue bars), whereas neither form was detected from the TET1 KO cells (2 biological replicates). f , Induction of hPGCLCs from wild-type (M1- BTAG ) and TET1 KO#1 and #2 hiPSCs. Photomicrographs of hiPSCs and iMeLC aggregates induced for hPGCLCs for 6 days (bright-field and fluorescence images for AG and BT) (left), their flow cytometric plots for AG and BT expression (middle), and percentages of BT + AG + cells (right) from each genotype are shown (4 biological replicates). Bar, 500 μm. g , Growth curves of BT + AG + cells and enrichment scores during BMP-driven (~c12: 25 ng/ml; c12~: 100 ng/ml) wild-type and TET1 KO#1 and #2 hPGCLC differentiation. 5 and 2 biological replicates for c12−c32 and for c42, respectively. The color coding is as indicated. h , UHC of the transcriptomes during hPGCLC induction and BMP-driven hPGCLC differentiation from wild-type and TET1 KO hiPSCs, with the expression levels of key genes indicated. The color coding is as indicated. i − k , The numbers of the differentially expressed genes (DEGs) [log 2 (RPM + 1) ≥ 3, fold change ≥ 2] between wild-type and TET1 KO cells (up- or down-regulated in TET1 KO cells) ( i ), UHC of the DEGs ( j ), and the GO enrichments and representative genes in the indicated DEG clusters ( k ). DEGs were defined using average expression values of biological replicates. The DEG numbers were unions of two comparisons (i.e., wild-type vs KO#1 and vs KO#2). Core ER genes were highlighted in red in ( j ). l , Box plots for the expression dynamics of ER genes (n = 42) during hPGCLC induction and BMP-driven hPGCLC differentiation from wild-type and TET1 KO hiPSCs. p -values of Two-sided Dunnet’s test (except c42) or paired two-sided t-test (c42) were shown. The upper hinges, lower hinges, and middle lines indicate 75 percentiles, 25 percentiles, and median values, respectively. The whiskers are drawn in length equal to the inter-quartile range (IQR) multiplied by 1.5. Data beyond the upper/lower whiskers are not shown.

Article Snippet: The membrane was incubated with rabbit anti-5hmC antibody (Active Motif, 39069) at 1:5,000 dilution or rabbit anti-5mC antibody (Sigma, SAB5600040) at 1:1,000 dilution in blocking buffer overnight at 4 °C.

Techniques: Knock-Out, Dot Blot, Derivative Assay, Fluorescence, Expressing

Journal: International Journal of Molecular Sciences

Article Title: Overexpression of a Novel Noxo1 Mutant Increases Ros Production and Noxo1 Relocalisation

doi: 10.3390/ijms24054663

Figure Lengend Snippet: Antibodies references used during the study.

Article Snippet: Anti Citrate synthase , Mouse , SC390693; SantaCruz Biotechnologies , 1/400 , .

Techniques: