Journal: bioRxiv

Article Title: TNF- α disrupts the malate-aspartate shuttle, driving metabolic rewiring in iPSC-derived enteric neural lineages from Parkinson’s Disease patients

doi: 10.1101/2025.03.25.644826

Figure Lengend Snippet: (A) Flow cytometry characterization of iPSC purity by staining of NANOG + /LIN28A + cells. Analysis was performed before starting the initial timepoint of differentiation (day 0). n=3 biological replicates per group, mean ± SEM. (B) Statistical quantification of the gene expression of neuronal marker TUBB3 , glial marker GFAP and enteric neuronal markers PHOX2B, ELAVL4 and HOXB3 in iPSC-derived ENLs at days 6, 40 and 70 of differentiation analyzed using RT-qPCR. Log2 fold change was calculated in relation to the Iso group at day 6 of differentiation. n=3 biological replicates per group, mean ± SEM, **p<0.01, ***p<0.001, ****p<0.0001, by two-way ANOVA with Tukey’s post-hoc. (C) UMAP plot obtained from scRNA-seq analysis of Iso and SNCA 3x ENLs at day 70 after start of differentiation, showing clustering of each cell line after batch effect correction. (D) UMAP plot obtained from scRNA-seq analysis of Iso and SNCA 3x ENLs at day 70 after start of differentiation, showing clusters identified after annotation. (E) Ridgeplot showing the expression of SNCA per condition considering each cluster identified. n=3 biological replicates per group, p values calculated by unpaired two-tailed Student’s t test. (F) Heatmap comparing the cellular communication between SNCA 3x and Iso ENLs in total cells, with the top color bar representing the sum of the column values displayed in incoming signals and the right color bar representing the sum of outgoing signals, red or blue indicating increased or decreased signal of SNCA 3x compared with Iso, respectively. Data was generated using CellChat. (G) Barplots showing the quantification of the number of inferred interactions (top) and interaction strength (bottom) in iPSC-ENLs total cells. Data was generated using CellChat. (H) Differences in the overall signaling pathway between SNCA 3x and Iso ENLs in total cells, with the ranking indicating the importance of the pathways; red indicating the signaling pathways enriched in Iso, blue representing the signaling pathways enriched SNCA 3x, and black representing no difference in signaling pathway enrichment in groups.

Article Snippet: For intracellular staining of iPSCs, we used a combination of Nanog (cat: 130-120-704, Miltenyi) and Lin28A (cat:563597, BD Biosciences) primary antibodies (both 1:100) in BD Perm/Wash Buffer for 30 minutes, followed by washing and resuspension in 300μl FACS buffer.

Techniques: Flow Cytometry, Staining, Gene Expression, Marker, Derivative Assay, Quantitative RT-PCR, Expressing, Two Tailed Test, Generated, Protein-Protein interactions

Journal: International journal of andrology

Article Title: TCam-2 seminoma cell line exhibits characteristic foetal germ cell responses to TGF-beta ligands and retinoic acid.

doi: 10.1111/j.1365-2605.2011.01170.x

Figure Lengend Snippet: Figure 1 Foetal germ cell and seminoma markers in TCam-2 cells. (a) The presence of transcripts characteristic of seminoma and foetal germ cells assessed by RT-PCR and Q-PCR in TCam-2 cells. For the RT-PCR (left panel) TCam-2 (T), HeLa cells (H) and human placenta (P) are indicated, alongside a control lacking reverse transcriptase (-). Amplification of b-actin was used as a loading control. Lower bands (arrowheads) correspond to unincorporated primers. OCT3 ⁄ 4, AP2g, KIT and low level KIT ligand (KITL) transcripts were detected in TCam-2 cells; two independent samples were tested, of which a representative sample is shown. Q-PCR (right panel) analysis of TCam-2 (T) and HeLa (H) cells. OCT3 ⁄ 4, AP2c, KIT and low level KITL transcripts were detected in TCam-2 cells. Three independent samples were analysed for each transcript, and data averaged with error bars indicating SEM. (b) Presence and subcellular localization of BLIMP1, OCT3 ⁄ 4, NANOG, KIT, VASA and DAZL1 proteins assayed in TCam-2 cells by immunofluorescence. Confocal imaging was performed at 40· magnification. The control images (no primary antibody control) are representative of all control immunofluorescence samples, in which no background signal was detected with the secondary antibodies alone. (c) A representative flow cytometric profile of TCam-2 and HeLa (KIT negative) cells stained for KIT (CD117). The top two panels are negative controls (no primary antibody present), whereas the lower two panels show intensity profiles representing KIT positive cells. No KIT-positive HeLa cells were detected. The mean fluorescence intensity of the whole cell population is indicated for each sample.

Article Snippet: Antibodies against human proteins: BLIMP1, STELLAR, VASA, DAZL1 (Abcam, Cambridge, MA, USA), OCT3 ⁄ 4, ACTRIB (ALK4), ACTRIIA, ACTRIIB, KIT (CD117) (Santa Cruz Biotechnology, Santa Cruz, CA), and NANOG (R&D systems, Inc) were verified to detect proteins of the appropriate size by Western blot (not shown) prior to use in immunofluorescence.

Techniques: Reverse Transcription Polymerase Chain Reaction, Control, Reverse Transcription, Imaging, Staining

Journal: Oncotarget

Article Title: Isolation and characterization of renal cancer stem cells from patient-derived xenografts

doi: 10.18632/oncotarget.6266

Figure Lengend Snippet: (A) Expression level of CD132, CD133, OCT3/4, NANOG, and EpCAM in RCC-41-PDX-1/CD132 + sorted cells. Results are representative of those obtained in three experiments. (B) Expression level of CD133, OCT-3/4, NANOG, and EpCAM in RCC-41-PDX-2/CD133 + and RCC-41-PDX-2/CD133 − sorted cells. Results are representative of those obtained in three experiments. For (A) and (B) , grey histograms correspond to cells incubated with the isotype-matched control antibody, and black outline histograms correspond to the analyzed markers. Grey numbers within panels correspond to Mean Fluorescence Intensity (MFI) of cells incubated with the isotype-matched control antibody, while black numbers correspond to MFI of the analyzed markers.

Article Snippet: Conjugated antibodies against NANOG (phycoerythrin (PE) conjugated goat polyclonal (IC1997P), 1:200 dilution), OCT-3/4 (PE conjugated goat polyclonal (IC1759P), 1:200 dilution), and Nestin (PE conjugated mouse monoclonal (IC1259P), 1:200 dilution) were purchased from R&D Systems Europe Ltd (Abingdon, UK).

Techniques: Expressing, Incubation, Control, Fluorescence

Journal: OncoTargets and therapy

Article Title: Integrated RNA Sequencing and Single-Cell Mass Cytometry Reveal a Novel Role of LncRNA HOXA-AS2 in Tumorigenesis and Stemness of Hepatocellular Carcinoma

doi: 10.2147/OTT.S272717

Figure Lengend Snippet: Purified Antibodies About the Stem-Like Cells Centric Panel

Article Snippet: NANOG , 169Tm , N31355 , Fluidigm , 3169014A.

Techniques: Purification