nih3t3 cell line  (ATCC)

Journal: Nature Communications

Article Title: Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework

doi: 10.1038/s41467-025-67016-9

Figure Lengend Snippet: a Schematic overview of data integration for multiple sci-mtChIL-seq datasets. RNAPII fragments were counted at the gene level and used as anchors to embed all datasets into a shared low-dimensional space. b Diagram of the skeletal muscle differentiation system using NIH3T3 TetOn3G/MyoD cells. c UMAP visualization of RNAPII counts at the single-cell level. Cells are colored by (left) sampling time point, (middle) paired epigenomic target, and (right) identified cluster. d Cell composition within each cluster. (Top) Distribution by sampling time. (Bottom) Distribution by paired target. e Heatmap of RNAPII accumulation across differentially expressed genes (DEGs). For each cluster, the top 200 cells (ranked by RNAPII count) and the top 50 DEGs (ranked by variance) are shown. f UMAP visualization of RNAPII accumulation levels per cell for representative DEGs. The values indicate niormalized counts of RNAPII for each coding region. g Gene Ontology (GO) enrichment analysis results for each cluster, based on the top 300 DEGs per cluster. h Heatmap showing mean accumulation levels of each epigenomic factor across clusters. i UMAP visualization of the accumulation levels per cell of epigenomic factors for representative DEGs.

Article Snippet: NIH3T3 Tet-On 3G/pCW-MyoD-Blast cells were cultured in DMEM supplemented with 10% Tet-Approved FBS (Takara; 631101).

Techniques: Sampling

Journal: Cell Death Discovery

Article Title: Sibiriline, a novel dual inhibitor of necroptosis and ferroptosis, prevents RIPK1 kinase activity and (phospho)lipid peroxidation as a potential therapeutic strategy

doi: 10.1038/s41420-025-02852-8

Figure Lengend Snippet: A SH-SY5Y cells were treated with either 10 µM Erastin, 5 µM RSL3, 10 µM FIN56 or 25 µM FINO 2 , and increasing concentrations of Sib up to 50 µM or until reaching maximal cellular viability or 1 µM of ferrostatin-1 (Fer-1/F1) as a control. Cell viability was determined after 24 h of treatment, using the MTS assay. The bar graph represents the mean of two replicates. B SH-SY5Y cells were co-treated for 24 h with 5 µM RSL3 and increasing concentrations of Sib or Fer-1. Cell death was estimated by the lactate dehydrogenase (LDH) release assay. Results are plotted in % of LDH release measured in cells treated with RSL3 alone (left axis, colored blue). Cell viability was evaluated by MTS reduction assay. Results obtained (colored red) were plotted as % of maximal viability with DMSO-treated cells (right axis). Data are shown as the mean +/- SEM of three replicates. C NIH3T3 cells were treated with either 1 µM RSL3, 5 ng/ml TNFα and 20 µM z-VAD.fmk (TZ) or a combination of both treatment (TZ + RSL3) and 10 µM of Sib or Nec-1f, 30 µM Nec-1s or 1 µM of Fer-1. Cell viability was evaluated by MTS reduction assay after 16 h of treatment. Data are shown as the mean ± SEM of three replicates of two independent experiments. D NIH3T3 cells were treated with 5 ng/ml TNFα, 20 µM z-VAD.fmk and 1 µM RSL3 and increasing concentrations of Sib or Nec-1f. Cell viability was determined after 16 h of treatment using an MTS assay. Data are shown as the mean ± SEM of two replicates. EC 50 values were calculated using graphpad prism software. Statistical analysis was performed using two-way ANOVA and Tukey’s multiple comparisons test using graphpad prism software. * p < 0.05, ** p < 0.01, *** p < 0.001 and **** p < 0.0001 vs controls.

Article Snippet: Human neuroblastoma SH-SY5Y cell line, human fibrosarcoma HT1080 cell line, mouse fibroblast NIH3T3 cell line and mouse hippocampal HT-22 cell line were originally obtained from American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Control, MTS Assay, Lactate Dehydrogenase Assay, Software

Journal: PLOS One

Article Title: A novel sialylation pathway mediated by extracellular vesicles in aggressive prostate cancer

doi: 10.1371/journal.pone.0329014

Figure Lengend Snippet: (A) IB analysis of ST6GAL1 and actin in PC3 and TRAMP-C2 TCL using 1 μg/mL (right panel) or 2 μg/mL (left panel) of ST6GAL1 antibody; 40 µg of TCLs were used. (B) IB analysis of ST6GAL1, CNX and PDL1 in TRAMP-C2, RM1 and NIH3T3 TCLs; 85 µg of TCLs were used. A lane loaded with non relevant sample is included (Non relevant).

Article Snippet: Additionally, murine prostate adenocarcinoma cell lines TRAMP-C2 (ATCC, CRL-2731, RRID:CVCL_3615) and RM1 (provided by Dr.T.Thompson, Baylor College of Medicine, Houston, Texas, USA, RRID: CVCL_B459), and the mouse fibroblast cell line NIH3T3 (ATCC, CRL-1658, RRID: CVCL_0594) were used.

Techniques:

Journal: EMBO Molecular Medicine

Article Title: Identification of p38 MAPK inhibition as a neuroprotective strategy for combinatorial SMA therapy

doi: 10.1038/s44321-025-00303-6

Figure Lengend Snippet: ( A ) Schematic of the chemical screen design. NIH3T3-SMN2/Smn RNAi cells were grown for 5 days in the presence of Dox prior to plating in 96-well format plates and addition of compounds from a chemical library. After an additional 5 days in culture in the presence of Dox, cells were fixed and stained with Hoechst, followed by automated whole-well imaging and determination of cell number. Created in BioRender. Pellizzoni, L. (2025) https://BioRender.com/k5m9uz6 . ( B ) Representative whole-well images of Dox-treated NIH3T3-SMN2/Smn RNAi cells cultured in 96-well format in the presence of vehicle (DMSO) or SMN-C3 (500 nM) for 4 h (Day 0) or 5 days (Day 5), followed by fixation and nuclear staining with Hoechst. ( C ) Graph summarizing the results of the chemical screen. Each point represents the effect of a single compound on the proliferation of NIH3T3-SMN2/Smn RNAi cells at day 5. The mean normalized cell number relative to vehicle-treated cells from three independent biological replicates is shown. The mean of the benchmark compound (SMN-C3) and the hit cutoff are indicated by dotted lines. Primary hits are shown in red, and the four compounds that passed secondary validation are labeled by name. ( D ) Dose-response analysis of the effects of the indicated compounds on cell proliferation in Dox-treated SMN2/Smn RNAi and Smn RNAi NIH3T3 cells. The graphs show mean and SEM ( n = 6 independent biological replicates) of normalized cell number relative to vehicle-treated cells at day 5 for each tested concentration, and non-linear curve fitting. .

Article Snippet: The NIH3T3 cell lines used in this study were previously described and generated from parental NIH3T3 cells that were obtained from the American Type Culture Collection (ATCC) without further authentication.

Techniques: Staining, Imaging, Cell Culture, Biomarker Discovery, Labeling, Concentration Assay

Journal: EMBO Molecular Medicine

Article Title: Identification of p38 MAPK inhibition as a neuroprotective strategy for combinatorial SMA therapy

doi: 10.1038/s44321-025-00303-6

Figure Lengend Snippet: ( A ) RT-qPCR analysis of Smn mRNA levels in untreated and Dox-treated NIH3T3-SMN2/Smn RNAi cells cultured for 5 days in the presence of either DMSO or EO1428, Clozapine, DHE and CGP7930 at a concentration of 10 μM. Mean, SEM, and individual values from Dox-treated cells normalized to DMSO-treated cells cultured without Dox are shown ( n = 3 independent biological replicates). One-way ANOVA followed by Tukey’s post hoc test. ns not significant. ( B ) RT-qPCR analysis of total (TOT) SMN2 mRNA levels in the same groups as in ( A ). Mean, SEM, and individual values from Dox-treated cells normalized to DMSO-treated cells cultured without Dox are shown ( n = 3 independent biological replicates). One-way ANOVA followed by Tukey’s post hoc test. ns, not significant. ( C ) RT-qPCR analysis of full-length (FL) SMN2 mRNA levels in the same groups as in ( A ). Mean, SEM, and individual values from Dox-treated cells normalized to DMSO-treated cells cultured without Dox are shown ( n = 3 independent biological replicates). One-way ANOVA followed by Tukey’s post hoc test. ns not significant. ( D ) Western blot analysis of SMN expression in the same groups as in ( A ). β-actin was used as a loading control. ( E ) Normalized mean, SEM, and individual values of SMN levels in Dox-treated relative to untreated NIH3T3-SMN2/Smn RNAi cells from three independent experiments as in ( D ). Kruskal–Wallis followed by Dunn’s post hoc test. ns not significant. ( F ) Western blot analysis of total and phosphorylated p38 MAPK in untreated and Dox-treated NIH3T3-SMN2/Smn RNAi cells. SMN and tubulin were used as controls. ( G ) Quantification of the levels of phosphorylated p38 MAPK relative to total p38 MAPK in NIH3T3-SMN2/Smn RNAi cells cultured with or without Dox from experiments as in ( B ). Normalized mean, SEM, and individual values from three independent biological replicates are shown. Two-tailed unpaired t -test. P = 0.031. ( H ) Dose-response analysis of the effects of the indicated p38 MAPK inhibitors on the proliferation of Dox-treated SMN2/Smn RNAi cells at day 5. The graphs show mean and SEM of normalized cell number relative to vehicle-treated cells at day 5 ( n = 6 biological replicates) for each tested concentration, and non-linear curve fitting. .

Article Snippet: The NIH3T3 cell lines used in this study were previously described and generated from parental NIH3T3 cells that were obtained from the American Type Culture Collection (ATCC) without further authentication.

Techniques: Quantitative RT-PCR, Cell Culture, Concentration Assay, Western Blot, Expressing, Control, Two Tailed Test