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matchmaker insert check pcr mix 1  (TaKaRa)


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    Structured Review

    TaKaRa matchmaker insert check pcr mix 1
    Matchmaker Insert Check Pcr Mix 1, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 78 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/insert/Matchmaker+Insert+Check+PCR+Mix+1/pm38672741-68-8-14
    Average 96 stars, based on 78 article reviews
    matchmaker insert check pcr mix 1 - by Bioz Stars, 2026-11
    96/100 stars

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    Related Articles

    Transformation Assay:

    Article Title: MYB44 Negatively Regulates GluTR1 to Inhibit Chlorophyll Synthesis in Cucumber Under High Temperature
    Article Snippet: system are the major sites of damage from high-temperature stress (Wang et al. 2024).. When lipid peroxidation occurs in the chloroplasts and thylakoid, it often leads to the degradation of chlorophyll (Chl).. Several studies have shown that high-temperature stress causes damage to thylakoid grana, resulting in significant Chl degradation, reduced enzyme activity, and impaired light energy capture (Kumarathunge et al. 2019; Jahan et al. 2021; Zahra et al. 2023).

    Article Title: SlAREB1 regulates ethylene biosynthesis and mediates the effect of abscisic acid on postharvest ripening of tomato fruit
    Article Snippet: .. Y1H assay was performed as per using YeastmakerTM Yeast Transformation System 2 (630439, Takara Biomedical Technology Co., Ltd., Beijing) and MatchmakerTM Insert Check PCR Mix 1 (630496, Takara Biomedical Technology Co., Ltd., Beijing). .. The promoter sequences of the selected genes were obtained by downloading from the Sol Genomics Network ( https://solgenomics.net ).

    Polymerase Chain Reaction:

    Article Title: MYB44 Negatively Regulates GluTR1 to Inhibit Chlorophyll Synthesis in Cucumber Under High Temperature
    Article Snippet: system are the major sites of damage from high-temperature stress (Wang et al. 2024).. When lipid peroxidation occurs in the chloroplasts and thylakoid, it often leads to the degradation of chlorophyll (Chl).. Several studies have shown that high-temperature stress causes damage to thylakoid grana, resulting in significant Chl degradation, reduced enzyme activity, and impaired light energy capture (Kumarathunge et al. 2019; Jahan et al. 2021; Zahra et al. 2023).

    Article Title: VvTPS14 is a linalool synthase activated by VvbZIP3 and repressed by VvMADS4.
    Article Snippet: Linalool is a key aromatic terpene that imparts the characteristic Muscat flavor in grape berries.. However, the upstream transcriptional mechanisms regulating its biosynthesis remain largely unknown.. Here, integrated GCMS and transcriptomic analyses across berry development in Muscat and non-Muscat cultivars identified VvTPS14 as a terpene synthase gene whose expression strongly correlated with the linalool accumulation pattern.

    Article Title: PrMYB5b drives geraniol biosynthesis by targeting PrDXS and PrGES in flare tree peony(Paeonia rockii (S.G.Haw & Lauener) T.Hong & J.J.Li ex D.Y.Hong) for high-value natural fragrance production
    Article Snippet: .. Genomic integration in yeast cells was confirmed by colony PCR with Matchmaker Insert Check PCR Mix 1 (Takara, Japan). .. Yeast one-hybrid assays were performed following the Matchmaker Gold Y1H System instructions (Takara, Japan).

    Article Title: Natural variation in ZmDapF1 enhances maize drought resilience.
    Article Snippet: As drought severely threatens the stability of crop yields, it is crucial to develop cultivars with enhanced drought resilience.. Here we demonstrate that natural variation in ZmDapF1, encoding a putative diaminopimelate epimerase, contributes to maize drought-stress resistance without compromising grain yield.. ZmDapF1 inhibits the activity of ZmMDH6, a chloroplast NADP-dependent malate dehydrogenase.

    Article Title: AdABI5 transcription factor promotes aroma synthesis in refrigerated kiwifruit via targeting Ad9sLOX and AdADH1
    Article Snippet: .. After 3 days 200 of dark cultivation at 30 °C, single colonies were picked for colony liquid PCR (Matchmaker 201 Insert Check PCR mix I, Cat. No. 630496, Takara Bio Inc., Mountain View, CA, USA) to identify 202 positive clones, while the untransformed Y1HGold strain served as a negative control. ..

    Article Title: The ABA signaling responsive gene VcCRF9 positively regulates anthocyanin synthesis in blueberry (Vaccinium corymbosum).
    Article Snippet: .. Recombinant yeast cells were first screened in SD/-Ura medium, and the yeast colony PCR assay was performed with Insert Check Mix1 (TaKaRa, Beijing, China, No. 630496) to obtain a positive plasmid. ..

    Article Title: Study on the formation mechanism of the key fresh aroma component (Z)-3-hexen-1-ol during the spreading process of lu'an Guapian green tea.
    Article Snippet: .. These strains were cultured on SD/-Ura solid medium at 30°C for 2–4 days to screen for positive clones, which were verified using Matchmaker Insert Check PCR Mix 1 (Takara, Dalian, China). ..

    Article Title: SlAREB1 regulates ethylene biosynthesis and mediates the effect of abscisic acid on postharvest ripening of tomato fruit
    Article Snippet: .. Y1H assay was performed as per using YeastmakerTM Yeast Transformation System 2 (630439, Takara Biomedical Technology Co., Ltd., Beijing) and MatchmakerTM Insert Check PCR Mix 1 (630496, Takara Biomedical Technology Co., Ltd., Beijing). .. The promoter sequences of the selected genes were obtained by downloading from the Sol Genomics Network ( https://solgenomics.net ).

    Concentration Assay:

    Article Title: VvTPS14 is a linalool synthase activated by VvbZIP3 and repressed by VvMADS4.
    Article Snippet: Linalool is a key aromatic terpene that imparts the characteristic Muscat flavor in grape berries.. However, the upstream transcriptional mechanisms regulating its biosynthesis remain largely unknown.. Here, integrated GCMS and transcriptomic analyses across berry development in Muscat and non-Muscat cultivars identified VvTPS14 as a terpene synthase gene whose expression strongly correlated with the linalool accumulation pattern.

    Activation Assay:

    Article Title: VvTPS14 is a linalool synthase activated by VvbZIP3 and repressed by VvMADS4.
    Article Snippet: Linalool is a key aromatic terpene that imparts the characteristic Muscat flavor in grape berries.. However, the upstream transcriptional mechanisms regulating its biosynthesis remain largely unknown.. Here, integrated GCMS and transcriptomic analyses across berry development in Muscat and non-Muscat cultivars identified VvTPS14 as a terpene synthase gene whose expression strongly correlated with the linalool accumulation pattern.

    Yeast:

    Article Title: PrMYB5b drives geraniol biosynthesis by targeting PrDXS and PrGES in flare tree peony(Paeonia rockii (S.G.Haw & Lauener) T.Hong & J.J.Li ex D.Y.Hong) for high-value natural fragrance production
    Article Snippet: .. Genomic integration in yeast cells was confirmed by colony PCR with Matchmaker Insert Check PCR Mix 1 (Takara, Japan). .. Yeast one-hybrid assays were performed following the Matchmaker Gold Y1H System instructions (Takara, Japan).

    Selection:

    Article Title: Natural variation in ZmDapF1 enhances maize drought resilience.
    Article Snippet: As drought severely threatens the stability of crop yields, it is crucial to develop cultivars with enhanced drought resilience.. Here we demonstrate that natural variation in ZmDapF1, encoding a putative diaminopimelate epimerase, contributes to maize drought-stress resistance without compromising grain yield.. ZmDapF1 inhibits the activity of ZmMDH6, a chloroplast NADP-dependent malate dehydrogenase.

    Clone Assay:

    Article Title: AdABI5 transcription factor promotes aroma synthesis in refrigerated kiwifruit via targeting Ad9sLOX and AdADH1
    Article Snippet: .. After 3 days 200 of dark cultivation at 30 °C, single colonies were picked for colony liquid PCR (Matchmaker 201 Insert Check PCR mix I, Cat. No. 630496, Takara Bio Inc., Mountain View, CA, USA) to identify 202 positive clones, while the untransformed Y1HGold strain served as a negative control. ..

    Article Title: Study on the formation mechanism of the key fresh aroma component (Z)-3-hexen-1-ol during the spreading process of lu'an Guapian green tea.
    Article Snippet: .. These strains were cultured on SD/-Ura solid medium at 30°C for 2–4 days to screen for positive clones, which were verified using Matchmaker Insert Check PCR Mix 1 (Takara, Dalian, China). ..

    Negative Control:

    Article Title: AdABI5 transcription factor promotes aroma synthesis in refrigerated kiwifruit via targeting Ad9sLOX and AdADH1
    Article Snippet: .. After 3 days 200 of dark cultivation at 30 °C, single colonies were picked for colony liquid PCR (Matchmaker 201 Insert Check PCR mix I, Cat. No. 630496, Takara Bio Inc., Mountain View, CA, USA) to identify 202 positive clones, while the untransformed Y1HGold strain served as a negative control. ..

    Recombinant:

    Article Title: The ABA signaling responsive gene VcCRF9 positively regulates anthocyanin synthesis in blueberry (Vaccinium corymbosum).
    Article Snippet: .. Recombinant yeast cells were first screened in SD/-Ura medium, and the yeast colony PCR assay was performed with Insert Check Mix1 (TaKaRa, Beijing, China, No. 630496) to obtain a positive plasmid. ..

    Plasmid Preparation:

    Article Title: The ABA signaling responsive gene VcCRF9 positively regulates anthocyanin synthesis in blueberry (Vaccinium corymbosum).
    Article Snippet: .. Recombinant yeast cells were first screened in SD/-Ura medium, and the yeast colony PCR assay was performed with Insert Check Mix1 (TaKaRa, Beijing, China, No. 630496) to obtain a positive plasmid. ..

    Cell Culture:

    Article Title: Study on the formation mechanism of the key fresh aroma component (Z)-3-hexen-1-ol during the spreading process of lu'an Guapian green tea.
    Article Snippet: .. These strains were cultured on SD/-Ura solid medium at 30°C for 2–4 days to screen for positive clones, which were verified using Matchmaker Insert Check PCR Mix 1 (Takara, Dalian, China). ..

    Y1H Assay:

    Article Title: SlAREB1 regulates ethylene biosynthesis and mediates the effect of abscisic acid on postharvest ripening of tomato fruit
    Article Snippet: .. Y1H assay was performed as per using YeastmakerTM Yeast Transformation System 2 (630439, Takara Biomedical Technology Co., Ltd., Beijing) and MatchmakerTM Insert Check PCR Mix 1 (630496, Takara Biomedical Technology Co., Ltd., Beijing). .. The promoter sequences of the selected genes were obtained by downloading from the Sol Genomics Network ( https://solgenomics.net ).



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    a Medium from freshly isolated organoids analysed by proteome array. n = 4 mice per group, pooled. Analysis: one-way ANOVA with Tukey’s correction. In bold: known NF-κB target genes. b Treg cell migration <t>transwell</t> assay: isolated MLN/ spleen primary Treg cells from Wt mice incubated with factors shown. NC (negative control – medium alone) or PC (positive control – Fetal bovine serum). Analysis: one-way ANOVA; Bonferroni’s multiple comparison test. Mean and SD shown. n = 9. c IHC against CCL22 ( n = 5 mice). Black triangles: CCL22+ immune cells. Purple triangles: CCL22+ epithelial cells. Scale: 10 μm. d Primary Treg cells from Wt mice cultured with organoid conditioned medium from Wt vs CCL22 −/− mice ( n = 3 mice), treated with LPS (25 μg/ml LPS over 48 h) or left untreated. Treg cell migration quantified via Transwell migration assay. Analysis: one-way ANOVA. Mean and SD shown. e Treg cell co-culture with conditioned organoid medium (SN), 30 Vol.-% and/or + 30 ng/mL murine IL-33, CM + 30 ng/mL IL-33 or CM + 100 ng/mL Amphiregulin. The fold change increase of expanded Treg cells on day 3 was measured in relation to the initial cell count. n = 3 mice. Analysis: as in a. Mean and SD shown. f Quantitation of CCR4+ and FoxP3+ cells from IF per image. n = 9. Mean and SD shown. g Isolated Wt ( n = 5) and IκBα IEC KO ( n = 3) CD4 + CD25+ Treg cells cultured for 6 h in medium supplemented with 50 ng/mL PMA and 1 µg/mL ionomycin. Supernatants analysed by ELISA. Analysis: unpaired t-test, two-sided. Mean and SD shown. h scRNA of colonic versus splenic immune cells from Wt and IκBα IEC KO mice. i Genes with significant changes in expression between colonic or splenic Treg cells in Wt versus IκBα IEC KO mice. j Differential expression of Gdpd3 and Ftl1 in spleen and colon Treg cells. Analysis: two-sided Wilcoxon rank-sum test k Colonic IF against GDPD3, CD4 and CDH1. Scale: 50 μm. n = 12. Zoom: double positive cells. l Quantitation of GDPD3+CD4+ cells per image. Analysis as in ( a ). Mean and SD shown. m Primary Treg cells from Wt mice cultured with organoid SN (supernatants). n = 3 mice. GDPD3+ cells visualized by IF. Analysis: as in ( a ). Mean and SD shown. Source data are provided as a Source Data file.
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    a Medium from freshly isolated organoids analysed by proteome array. n = 4 mice per group, pooled. Analysis: one-way ANOVA with Tukey’s correction. In bold: known NF-κB target genes. b Treg cell migration <t>transwell</t> assay: isolated MLN/ spleen primary Treg cells from Wt mice incubated with factors shown. NC (negative control – medium alone) or PC (positive control – Fetal bovine serum). Analysis: one-way ANOVA; Bonferroni’s multiple comparison test. Mean and SD shown. n = 9. c IHC against CCL22 ( n = 5 mice). Black triangles: CCL22+ immune cells. Purple triangles: CCL22+ epithelial cells. Scale: 10 μm. d Primary Treg cells from Wt mice cultured with organoid conditioned medium from Wt vs CCL22 −/− mice ( n = 3 mice), treated with LPS (25 μg/ml LPS over 48 h) or left untreated. Treg cell migration quantified via Transwell migration assay. Analysis: one-way ANOVA. Mean and SD shown. e Treg cell co-culture with conditioned organoid medium (SN), 30 Vol.-% and/or + 30 ng/mL murine IL-33, CM + 30 ng/mL IL-33 or CM + 100 ng/mL Amphiregulin. The fold change increase of expanded Treg cells on day 3 was measured in relation to the initial cell count. n = 3 mice. Analysis: as in a. Mean and SD shown. f Quantitation of CCR4+ and FoxP3+ cells from IF per image. n = 9. Mean and SD shown. g Isolated Wt ( n = 5) and IκBα IEC KO ( n = 3) CD4 + CD25+ Treg cells cultured for 6 h in medium supplemented with 50 ng/mL PMA and 1 µg/mL ionomycin. Supernatants analysed by ELISA. Analysis: unpaired t-test, two-sided. Mean and SD shown. h scRNA of colonic versus splenic immune cells from Wt and IκBα IEC KO mice. i Genes with significant changes in expression between colonic or splenic Treg cells in Wt versus IκBα IEC KO mice. j Differential expression of Gdpd3 and Ftl1 in spleen and colon Treg cells. Analysis: two-sided Wilcoxon rank-sum test k Colonic IF against GDPD3, CD4 and CDH1. Scale: 50 μm. n = 12. Zoom: double positive cells. l Quantitation of GDPD3+CD4+ cells per image. Analysis as in ( a ). Mean and SD shown. m Primary Treg cells from Wt mice cultured with organoid SN (supernatants). n = 3 mice. GDPD3+ cells visualized by IF. Analysis: as in ( a ). Mean and SD shown. Source data are provided as a Source Data file.
    Non Coding Insert, supplied by Addgene inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    a Medium from freshly isolated organoids analysed by proteome array. n = 4 mice per group, pooled. Analysis: one-way ANOVA with Tukey’s correction. In bold: known NF-κB target genes. b Treg cell migration <t>transwell</t> assay: isolated MLN/ spleen primary Treg cells from Wt mice incubated with factors shown. NC (negative control – medium alone) or PC (positive control – Fetal bovine serum). Analysis: one-way ANOVA; Bonferroni’s multiple comparison test. Mean and SD shown. n = 9. c IHC against CCL22 ( n = 5 mice). Black triangles: CCL22+ immune cells. Purple triangles: CCL22+ epithelial cells. Scale: 10 μm. d Primary Treg cells from Wt mice cultured with organoid conditioned medium from Wt vs CCL22 −/− mice ( n = 3 mice), treated with LPS (25 μg/ml LPS over 48 h) or left untreated. Treg cell migration quantified via Transwell migration assay. Analysis: one-way ANOVA. Mean and SD shown. e Treg cell co-culture with conditioned organoid medium (SN), 30 Vol.-% and/or + 30 ng/mL murine IL-33, CM + 30 ng/mL IL-33 or CM + 100 ng/mL Amphiregulin. The fold change increase of expanded Treg cells on day 3 was measured in relation to the initial cell count. n = 3 mice. Analysis: as in a. Mean and SD shown. f Quantitation of CCR4+ and FoxP3+ cells from IF per image. n = 9. Mean and SD shown. g Isolated Wt ( n = 5) and IκBα IEC KO ( n = 3) CD4 + CD25+ Treg cells cultured for 6 h in medium supplemented with 50 ng/mL PMA and 1 µg/mL ionomycin. Supernatants analysed by ELISA. Analysis: unpaired t-test, two-sided. Mean and SD shown. h scRNA of colonic versus splenic immune cells from Wt and IκBα IEC KO mice. i Genes with significant changes in expression between colonic or splenic Treg cells in Wt versus IκBα IEC KO mice. j Differential expression of Gdpd3 and Ftl1 in spleen and colon Treg cells. Analysis: two-sided Wilcoxon rank-sum test k Colonic IF against GDPD3, CD4 and CDH1. Scale: 50 μm. n = 12. Zoom: double positive cells. l Quantitation of GDPD3+CD4+ cells per image. Analysis as in ( a ). Mean and SD shown. m Primary Treg cells from Wt mice cultured with organoid SN (supernatants). n = 3 mice. GDPD3+ cells visualized by IF. Analysis: as in ( a ). Mean and SD shown. Source data are provided as a Source Data file.
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    Illumina Inc illumina short insert libraries
    a Medium from freshly isolated organoids analysed by proteome array. n = 4 mice per group, pooled. Analysis: one-way ANOVA with Tukey’s correction. In bold: known NF-κB target genes. b Treg cell migration <t>transwell</t> assay: isolated MLN/ spleen primary Treg cells from Wt mice incubated with factors shown. NC (negative control – medium alone) or PC (positive control – Fetal bovine serum). Analysis: one-way ANOVA; Bonferroni’s multiple comparison test. Mean and SD shown. n = 9. c IHC against CCL22 ( n = 5 mice). Black triangles: CCL22+ immune cells. Purple triangles: CCL22+ epithelial cells. Scale: 10 μm. d Primary Treg cells from Wt mice cultured with organoid conditioned medium from Wt vs CCL22 −/− mice ( n = 3 mice), treated with LPS (25 μg/ml LPS over 48 h) or left untreated. Treg cell migration quantified via Transwell migration assay. Analysis: one-way ANOVA. Mean and SD shown. e Treg cell co-culture with conditioned organoid medium (SN), 30 Vol.-% and/or + 30 ng/mL murine IL-33, CM + 30 ng/mL IL-33 or CM + 100 ng/mL Amphiregulin. The fold change increase of expanded Treg cells on day 3 was measured in relation to the initial cell count. n = 3 mice. Analysis: as in a. Mean and SD shown. f Quantitation of CCR4+ and FoxP3+ cells from IF per image. n = 9. Mean and SD shown. g Isolated Wt ( n = 5) and IκBα IEC KO ( n = 3) CD4 + CD25+ Treg cells cultured for 6 h in medium supplemented with 50 ng/mL PMA and 1 µg/mL ionomycin. Supernatants analysed by ELISA. Analysis: unpaired t-test, two-sided. Mean and SD shown. h scRNA of colonic versus splenic immune cells from Wt and IκBα IEC KO mice. i Genes with significant changes in expression between colonic or splenic Treg cells in Wt versus IκBα IEC KO mice. j Differential expression of Gdpd3 and Ftl1 in spleen and colon Treg cells. Analysis: two-sided Wilcoxon rank-sum test k Colonic IF against GDPD3, CD4 and CDH1. Scale: 50 μm. n = 12. Zoom: double positive cells. l Quantitation of GDPD3+CD4+ cells per image. Analysis as in ( a ). Mean and SD shown. m Primary Treg cells from Wt mice cultured with organoid SN (supernatants). n = 3 mice. GDPD3+ cells visualized by IF. Analysis: as in ( a ). Mean and SD shown. Source data are provided as a Source Data file.
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    a Medium from freshly isolated organoids analysed by proteome array. n = 4 mice per group, pooled. Analysis: one-way ANOVA with Tukey’s correction. In bold: known NF-κB target genes. b Treg cell migration <t>transwell</t> assay: isolated MLN/ spleen primary Treg cells from Wt mice incubated with factors shown. NC (negative control – medium alone) or PC (positive control – Fetal bovine serum). Analysis: one-way ANOVA; Bonferroni’s multiple comparison test. Mean and SD shown. n = 9. c IHC against CCL22 ( n = 5 mice). Black triangles: CCL22+ immune cells. Purple triangles: CCL22+ epithelial cells. Scale: 10 μm. d Primary Treg cells from Wt mice cultured with organoid conditioned medium from Wt vs CCL22 −/− mice ( n = 3 mice), treated with LPS (25 μg/ml LPS over 48 h) or left untreated. Treg cell migration quantified via Transwell migration assay. Analysis: one-way ANOVA. Mean and SD shown. e Treg cell co-culture with conditioned organoid medium (SN), 30 Vol.-% and/or + 30 ng/mL murine IL-33, CM + 30 ng/mL IL-33 or CM + 100 ng/mL Amphiregulin. The fold change increase of expanded Treg cells on day 3 was measured in relation to the initial cell count. n = 3 mice. Analysis: as in a. Mean and SD shown. f Quantitation of CCR4+ and FoxP3+ cells from IF per image. n = 9. Mean and SD shown. g Isolated Wt ( n = 5) and IκBα IEC KO ( n = 3) CD4 + CD25+ Treg cells cultured for 6 h in medium supplemented with 50 ng/mL PMA and 1 µg/mL ionomycin. Supernatants analysed by ELISA. Analysis: unpaired t-test, two-sided. Mean and SD shown. h scRNA of colonic versus splenic immune cells from Wt and IκBα IEC KO mice. i Genes with significant changes in expression between colonic or splenic Treg cells in Wt versus IκBα IEC KO mice. j Differential expression of Gdpd3 and Ftl1 in spleen and colon Treg cells. Analysis: two-sided Wilcoxon rank-sum test k Colonic IF against GDPD3, CD4 and CDH1. Scale: 50 μm. n = 12. Zoom: double positive cells. l Quantitation of GDPD3+CD4+ cells per image. Analysis as in ( a ). Mean and SD shown. m Primary Treg cells from Wt mice cultured with organoid SN (supernatants). n = 3 mice. GDPD3+ cells visualized by IF. Analysis: as in ( a ). Mean and SD shown. Source data are provided as a Source Data file.
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    a Medium from freshly isolated organoids analysed by proteome array. n = 4 mice per group, pooled. Analysis: one-way ANOVA with Tukey’s correction. In bold: known NF-κB target genes. b Treg cell migration transwell assay: isolated MLN/ spleen primary Treg cells from Wt mice incubated with factors shown. NC (negative control – medium alone) or PC (positive control – Fetal bovine serum). Analysis: one-way ANOVA; Bonferroni’s multiple comparison test. Mean and SD shown. n = 9. c IHC against CCL22 ( n = 5 mice). Black triangles: CCL22+ immune cells. Purple triangles: CCL22+ epithelial cells. Scale: 10 μm. d Primary Treg cells from Wt mice cultured with organoid conditioned medium from Wt vs CCL22 −/− mice ( n = 3 mice), treated with LPS (25 μg/ml LPS over 48 h) or left untreated. Treg cell migration quantified via Transwell migration assay. Analysis: one-way ANOVA. Mean and SD shown. e Treg cell co-culture with conditioned organoid medium (SN), 30 Vol.-% and/or + 30 ng/mL murine IL-33, CM + 30 ng/mL IL-33 or CM + 100 ng/mL Amphiregulin. The fold change increase of expanded Treg cells on day 3 was measured in relation to the initial cell count. n = 3 mice. Analysis: as in a. Mean and SD shown. f Quantitation of CCR4+ and FoxP3+ cells from IF per image. n = 9. Mean and SD shown. g Isolated Wt ( n = 5) and IκBα IEC KO ( n = 3) CD4 + CD25+ Treg cells cultured for 6 h in medium supplemented with 50 ng/mL PMA and 1 µg/mL ionomycin. Supernatants analysed by ELISA. Analysis: unpaired t-test, two-sided. Mean and SD shown. h scRNA of colonic versus splenic immune cells from Wt and IκBα IEC KO mice. i Genes with significant changes in expression between colonic or splenic Treg cells in Wt versus IκBα IEC KO mice. j Differential expression of Gdpd3 and Ftl1 in spleen and colon Treg cells. Analysis: two-sided Wilcoxon rank-sum test k Colonic IF against GDPD3, CD4 and CDH1. Scale: 50 μm. n = 12. Zoom: double positive cells. l Quantitation of GDPD3+CD4+ cells per image. Analysis as in ( a ). Mean and SD shown. m Primary Treg cells from Wt mice cultured with organoid SN (supernatants). n = 3 mice. GDPD3+ cells visualized by IF. Analysis: as in ( a ). Mean and SD shown. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Epithelial NF-κB shapes protective Treg cell responses to restrain intestinal inflammation

    doi: 10.1038/s41467-026-78796-z

    Figure Lengend Snippet: a Medium from freshly isolated organoids analysed by proteome array. n = 4 mice per group, pooled. Analysis: one-way ANOVA with Tukey’s correction. In bold: known NF-κB target genes. b Treg cell migration transwell assay: isolated MLN/ spleen primary Treg cells from Wt mice incubated with factors shown. NC (negative control – medium alone) or PC (positive control – Fetal bovine serum). Analysis: one-way ANOVA; Bonferroni’s multiple comparison test. Mean and SD shown. n = 9. c IHC against CCL22 ( n = 5 mice). Black triangles: CCL22+ immune cells. Purple triangles: CCL22+ epithelial cells. Scale: 10 μm. d Primary Treg cells from Wt mice cultured with organoid conditioned medium from Wt vs CCL22 −/− mice ( n = 3 mice), treated with LPS (25 μg/ml LPS over 48 h) or left untreated. Treg cell migration quantified via Transwell migration assay. Analysis: one-way ANOVA. Mean and SD shown. e Treg cell co-culture with conditioned organoid medium (SN), 30 Vol.-% and/or + 30 ng/mL murine IL-33, CM + 30 ng/mL IL-33 or CM + 100 ng/mL Amphiregulin. The fold change increase of expanded Treg cells on day 3 was measured in relation to the initial cell count. n = 3 mice. Analysis: as in a. Mean and SD shown. f Quantitation of CCR4+ and FoxP3+ cells from IF per image. n = 9. Mean and SD shown. g Isolated Wt ( n = 5) and IκBα IEC KO ( n = 3) CD4 + CD25+ Treg cells cultured for 6 h in medium supplemented with 50 ng/mL PMA and 1 µg/mL ionomycin. Supernatants analysed by ELISA. Analysis: unpaired t-test, two-sided. Mean and SD shown. h scRNA of colonic versus splenic immune cells from Wt and IκBα IEC KO mice. i Genes with significant changes in expression between colonic or splenic Treg cells in Wt versus IκBα IEC KO mice. j Differential expression of Gdpd3 and Ftl1 in spleen and colon Treg cells. Analysis: two-sided Wilcoxon rank-sum test k Colonic IF against GDPD3, CD4 and CDH1. Scale: 50 μm. n = 12. Zoom: double positive cells. l Quantitation of GDPD3+CD4+ cells per image. Analysis as in ( a ). Mean and SD shown. m Primary Treg cells from Wt mice cultured with organoid SN (supernatants). n = 3 mice. GDPD3+ cells visualized by IF. Analysis: as in ( a ). Mean and SD shown. Source data are provided as a Source Data file.

    Article Snippet: 4.5 × 10 4 cells/well were seeded in RPMI medium without additives on a transwell insert (8μm pore size, Greiner Bio-One Cat. 662638) in a 24- well plate.

    Techniques: Isolation, Organoids, Analysis, Migration, Transwell Assay, Incubation, Negative Control, Positive Control, Comparison, Cell Culture, Transwell Migration Assay, Co-culture Assay, Cell Characterization, Quantitation Assay, Enzyme-linked Immunosorbent Assay, Expressing, Quantitative Proteomics

    a scRNA dataset ( GSE116222 ) is based on samples from inflamed and non-inflamed colon regions of UC patients, as well as those from healthy controls. Visualization of IEC cells across the three conditions. b TRRUST analysis of top upregulated TF networks across the three conditions (Healthy, UC and UC NI (non-inflamed)) in IEC presented as a volcano plot. Text in blue: factors belonging to the NF-κB axis. A Gene-set enrichment was performed using Enrichr. Enrichment significance was assessed using Fisher’s exact test, and enrichment magnitude was represented by the odds ratio. Volcano plots generated with the Enrichr Appyter display odds ratio versus −log 10 ( P value). c TRRUST analysis of downregulated TF networks in UC-inflamed colon IEC versus healthy IEC. Text in blue: factors belonging to the NF-κB axis. Analysis as in ( b ). d H&E of colon sections from healthy and UC patients. Scale: 50 μm. e Colitis score (Nancy index) from ( d ). The patient number is shown in the graph. Analysis: Two-tailed t -test. Mean and SD shown. f Colon-derived organoids were derived from colon biopsies of UC patients or non-IBD controls, with at least n = 4 patients per group. Growth of colon organoids was measured over several days. Mean and SD shown. Analysis: t- test, two-tailed, unpaired. g At least 10 colon organoids per patient from healthy ( n = 3 persons) and UC colon-derived organoids ( n = 4 patients) treated with LPS over 48 h and stained with antibodies as indicated. Scale: 50 μm. h Quantification from g. Top panel: Ki67 (not significant). Lower panel: cleaved caspase 3. Analysis: One-way ANOVA with Tukey’s correction. Mean and SD shown. i Colon organoids were treated with TNF (TNF was removed, and the medium was changed) or left untreated. Medium from colon-derived organoids was analysed by proteome array, and the presence of secreted factors quantitated from bulk ( n = 4) samples per group and n = 2 technical replicates. Significance determined by one-way ANOVA with Tukey’s correction. Only significant results are shown. j Analysis of proteome data by DAVID v2023q4 followed by REVIGO for visualization of GO terms on semantic space. Bubble size indicates prevalence. Color: orange—terms enriched in medium of UC colon-derived organoids treated with TNF, purple—terms enriched in medium of healthy colon-derived organoids treated with TNF. SD and mean shown. Analysis: Welch’s t -test, two-sided – no significance. k Transwell recruitment with Jurkat cells incubated in medium from colon-derived organoids from UC patients or healthy controls. Analysis: one-way ANOVA with Tukey’s correction. n = 4 for healthy samples and n = 6 for UC samples (pooled). Individual points indicate technical replicates. Mean and SD shown. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Epithelial NF-κB shapes protective Treg cell responses to restrain intestinal inflammation

    doi: 10.1038/s41467-026-78796-z

    Figure Lengend Snippet: a scRNA dataset ( GSE116222 ) is based on samples from inflamed and non-inflamed colon regions of UC patients, as well as those from healthy controls. Visualization of IEC cells across the three conditions. b TRRUST analysis of top upregulated TF networks across the three conditions (Healthy, UC and UC NI (non-inflamed)) in IEC presented as a volcano plot. Text in blue: factors belonging to the NF-κB axis. A Gene-set enrichment was performed using Enrichr. Enrichment significance was assessed using Fisher’s exact test, and enrichment magnitude was represented by the odds ratio. Volcano plots generated with the Enrichr Appyter display odds ratio versus −log 10 ( P value). c TRRUST analysis of downregulated TF networks in UC-inflamed colon IEC versus healthy IEC. Text in blue: factors belonging to the NF-κB axis. Analysis as in ( b ). d H&E of colon sections from healthy and UC patients. Scale: 50 μm. e Colitis score (Nancy index) from ( d ). The patient number is shown in the graph. Analysis: Two-tailed t -test. Mean and SD shown. f Colon-derived organoids were derived from colon biopsies of UC patients or non-IBD controls, with at least n = 4 patients per group. Growth of colon organoids was measured over several days. Mean and SD shown. Analysis: t- test, two-tailed, unpaired. g At least 10 colon organoids per patient from healthy ( n = 3 persons) and UC colon-derived organoids ( n = 4 patients) treated with LPS over 48 h and stained with antibodies as indicated. Scale: 50 μm. h Quantification from g. Top panel: Ki67 (not significant). Lower panel: cleaved caspase 3. Analysis: One-way ANOVA with Tukey’s correction. Mean and SD shown. i Colon organoids were treated with TNF (TNF was removed, and the medium was changed) or left untreated. Medium from colon-derived organoids was analysed by proteome array, and the presence of secreted factors quantitated from bulk ( n = 4) samples per group and n = 2 technical replicates. Significance determined by one-way ANOVA with Tukey’s correction. Only significant results are shown. j Analysis of proteome data by DAVID v2023q4 followed by REVIGO for visualization of GO terms on semantic space. Bubble size indicates prevalence. Color: orange—terms enriched in medium of UC colon-derived organoids treated with TNF, purple—terms enriched in medium of healthy colon-derived organoids treated with TNF. SD and mean shown. Analysis: Welch’s t -test, two-sided – no significance. k Transwell recruitment with Jurkat cells incubated in medium from colon-derived organoids from UC patients or healthy controls. Analysis: one-way ANOVA with Tukey’s correction. n = 4 for healthy samples and n = 6 for UC samples (pooled). Individual points indicate technical replicates. Mean and SD shown. Source data are provided as a Source Data file.

    Article Snippet: 4.5 × 10 4 cells/well were seeded in RPMI medium without additives on a transwell insert (8μm pore size, Greiner Bio-One Cat. 662638) in a 24- well plate.

    Techniques: Analysis, Generated, Two Tailed Test, Derivative Assay, Organoids, Staining, Incubation, Significance Assay