Journal: Cell Research

Article Title: Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

doi: 10.1038/s41422-020-0374-x

Figure Lengend Snippet: a t-SNE plot showing 10 clusters of 17,263 T/NK cells (indicated by colors). b t-SNE plot, color coding for the expression of the marker genes (gray to red) for the indicated cell subtypes. c Average expression of selected T cell function-associated genes of naïve markers, inhibitory receptors, cytokines and effector molecules, co-stimulatory molecules, and Treg markers in each cell cluster. d Potential developmental trajectory of CD4 + T cells ( n = 5694) inferred by analysis with Monocle 2. Arrows show the increasing directions of certain CD4 + T cell properties annotated with the signatures shown in e . e Traceplots of (left) CD4 + T cell activation signature along activation component and (right) terminal differentiation signature along terminal differentiation component for the CD4 + T cells. Cells are projected along the component, with the blue line indicating the moving average of the expression of signatures (a sliding window of length equal to 5% of the total number of CD4 + T cells was used), and the shaded area displaying SEM. Signatures used are presented in Supplementary information, Table . f Potential developmental trajectory of CD8 + T cells ( n = 6975) inferred by analysis with Monocle 2. Arrows show the increasing directions of certain CD8 + T cell properties annotated with the signatures shown in g . g Traceplots (as in e ) of (left) CD8 + T cell activation signature along activation component and (right) terminal differentiation signature along terminal differentiation component for the CD8 + T cells. Signatures used are presented in Supplementary information, Table . h Spearman correlation between the activity of CD8 + T cells ( n = 6975), as measured by average granzyme expression ( GZMA , GZMB and GZMH ), and the expression of CD8 + T cell-specific genes. Genes encoding known immune checkpoint molecules are highlighted in blue. CD4 + T conv , conventional CD4 + T cell; CD8 + T dys , dysfunctional CD8 + T cell; NK, natural killer. i Heatmap showing the activity of TFs in each T/NK cell subtype. The TF activity is scored using AUCell. j Peripheral CD8 + T cells and NK cells were transfected with negative control (NC), EOMES-specific, RUNX3-specific, or XBP1-specific siRNAs, followed by immunoblot analysis to determine protein expression of Eomes, Runx3, or XBP1. β-actin is the loading control. The experiments were repeated independently for three times with similar results. k Left, representative histograms depicting the expression of GZMB and perforin on peripheral CD8 + T cells transfected with NC and EOMES-specific ( n = 6 donors, n = 5 independent experiments), RUNX3-specific ( n = 6 donors, n = 6 independent experiments), and XBP1-specific siRNAs ( n = 6 donors, n = 5 independent experiments). Right, percentage of GZMB + or perforin + cells in siNC and siEOMES ( n = 6), siRUNX3 ( n = 6), and siXBP1 ( n = 6) CD8 + T cells. l Left, representative histograms depicting the expression of GZMB and perforin on peripheral NK cells transfected with NC and EOMES-specific ( n = 6 donors, n = 5 independent experiments), RUNX3-specific ( n = 6 donors, n = 5 independent experiments), and XBP1-specific siRNAs ( n = 6 donors, n = 5 independent experiments). Right, percentage of GZMB + or perforin + cells in siNC and siEOMES ( n = 6), siRUNX3 ( n = 6), and siXBP1 ( n = 6) NK cells. * P < 0.05, ** P < 0.01 (paired Student’s t -test).

Article Snippet: The following antibodies were used in immunoblotting: anti-NR1H3 (Rabbit, ab176323, dilution 1:1000; Abcam), anti-TFEC (Rabbit, ab185226, dilution 1:1000; Abcam), anti-EOMES (Rabbit, 81493s, dilution 1:1000; CST), anti-RUNX3 (Rabbit, ab224641, dilution 1:1000; Abcam), anti-XBP1 (Rabbit, ab109221, dilution 1:1000; Abcam), and anti-β-actin (mouse, 3700s, dilution 1:1000; CST).

Techniques: Expressing, Marker, Cell Function Assay, Activation Assay, Activity Assay, Transfection, Negative Control, Western Blot

Journal: Integrative Biology

Article Title: Rapid translocation of pluripotency-related transcription factors by external uniaxial forces

doi: 10.1093/intbio/zyz003

Figure Lengend Snippet: List of primary antibodies.

Article Snippet: EOMES , Cell Signaling , #81493S , 1:200.

Techniques:

Journal: Integrative Biology

Article Title: Rapid translocation of pluripotency-related transcription factors by external uniaxial forces

doi: 10.1093/intbio/zyz003

Figure Lengend Snippet: Molecular characterization and identification of 10% strain applied human ESCs for 2 h via qRT-PCR analysis for temporal expression of (A) pluripotency (NANOG, OCT4, SOX2, and KLF4), (B) trophoctoderm markers (CDX2, EOMES, EpCAM, and FGF4), (C) ecto- and endodermal lineage differentiation (WNT3A, SOX17, GATA6, and PAX6), and (D) cytoskeletal, focal adhesion kinase (Ptk2) and PXN (Paxillin), Integrin alpha 6 (ITGA6) and E-CADHERIN with and without 10% strain. All quantification from three independent replicates. Unpaired t test P values <0.05 (*), <0.01 (**), <0.001(***), n.s.: not significant.

Article Snippet: Primary antibodies for immunofluorescence in Table . table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Antibody name Company Catalog number Dilutions OCT4 SantaCruz #sc8629 1:500 NANOG Abcam #ab62724 1:100 SOX2 Millipore #ab56603 1:500 PFAK (TYR397) Invitrogen #700255 1:200 CDX2 SantaCruz #393572 1:500 KLF4 ABCAM #ab129473 1:200 E-CADHERIN R&D Systems #AF748 1:500 INTEGRIN ALPHA 6 SantaCruz #374057 1:500 EOMES Cell Signaling #81493S 1:200 EPCAM Cell Signaling #2929S 1:300 pERK Cell Signaling #9101 1:250 Open in a separate window List of primary antibodies.

Techniques: Quantitative RT-PCR, Expressing

Journal: Integrative Biology

Article Title: Rapid translocation of pluripotency-related transcription factors by external uniaxial forces

doi: 10.1093/intbio/zyz003

Figure Lengend Snippet: List of primary antibodies.

Article Snippet: Primary antibodies for immunofluorescence in Table . table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Antibody name Company Catalog number Dilutions OCT4 SantaCruz #sc8629 1:500 NANOG Abcam #ab62724 1:100 SOX2 Millipore #ab56603 1:500 PFAK (TYR397) Invitrogen #700255 1:200 CDX2 SantaCruz #393572 1:500 KLF4 ABCAM #ab129473 1:200 E-CADHERIN R&D Systems #AF748 1:500 INTEGRIN ALPHA 6 SantaCruz #374057 1:500 EOMES Cell Signaling #81493S 1:200 EPCAM Cell Signaling #2929S 1:300 pERK Cell Signaling #9101 1:250 Open in a separate window List of primary antibodies.

Techniques: