Journal: Cell

Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

doi: 10.1016/j.cell.2018.08.067

Figure Lengend Snippet: Human Colonic Mesenchymal Heterogeneity in Health (A) Flow cytometry analysis of the indicated surface markers on colonic single-cell suspensions following removal of epithelial and hematopoietic cells by MACS. Column flow-through is shown in red, and column-retained fraction is in blue. (B) t-SNE plot of the healthy human colonic mesenchyme dataset. Single cells colored by cluster annotation. (C) Violin plots for pan-fibroblast marker genes vimentin ( VIM ) and collagen types 1 and 3 ( COL1A2 , COL3A1 ) across clusters. (D) Violin plots for high-ranked transcriptional regulators and marker genes sharing GO annotation for significantly enriched terms for (i) S1 subset, (ii) S2 subset, (iii) S3 subset, (iv) S4 subset, and (v) myofibroblasts. Crossbars indicate median expression. (E) Single-molecule ISH staining of healthy human colonic tissue showing distribution of S1 markers ( ADAMDEC1 , DCN , SLIT2 , and CXCL12 ) (left) and S2 markers ( F3 (CD142) , WNT5A , HSD17B2 , WNT5B , POSTN , BMP2 , FRZB , BMP5 ) (right). (F) Identification of SOX6 − ZEB2 + /ZEB1 − ZEB2 + S1 and SOX6 + ZEB2 − /ZEB1 + ZEB2 − S2 subsets in healthy human colon. (G) Single (left) and co-staining with CD45 (right) and F3/CD142 (S2), ZEB2 (S1), and SMAD7 (S3) by IHC in colonic sections. The lower far-right panel is a quadruple stain of all 4 markers. (H) Differential expression analysis between S2a and S2b reveals 302 differentially expressed genes. (I) t-SNE plots showing examples of genes differentially expressed between S2a and S2b. (J) GO enrichment terms for S2a and S2b. See also – and – .

Article Snippet: Mouse monoclonal anti-human ZEB2/SIP1 , Bio-Techne , Cat#MAB73782; RRID: AB_2737260.

Techniques: Flow Cytometry, Marker, Expressing, Staining

Journal: Cell

Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

doi: 10.1016/j.cell.2018.08.067

Figure Lengend Snippet:

Article Snippet: Mouse monoclonal anti-human ZEB2/SIP1 , Bio-Techne , Cat#MAB73782; RRID: AB_2737260.

Techniques: Recombinant, Coagulation, Antibody Labeling, Membrane, Plasmid Preparation, Polymer, Blocking Assay, Staining, Imaging, Software, Hybridization

Journal: Cell

Article Title: An early cell shape transition drives evolutionary expansion of the human forebrain

doi: 10.1016/j.cell.2021.02.050

Figure Lengend Snippet:

Article Snippet: mouse anti-ZEB2 , Origene , Cat# TA802113, RRID: AB_2616296.

Techniques: Fluorescence, Recombinant, Knock-Out, Protease Inhibitor, Multiplex Assay, Software

Journal: Cancer research

Article Title: GSK 3 inhibition drives maturation of NK cells and enhances their antitumor activity

doi: 10.1158/0008-5472.CAN-17-0799

Figure Lengend Snippet: CD3/19-depleted PBMCs from CMV seropositive donors were cultured for 7 days with 10 ng/ml IL-15 and either DMSO or 5 μM CHIR99021 (n = 9). CD3−CD56+ NK cells were then isolated from each culture condition and analyzed by A, qRT-PCR for expression of TBX21, ZEB2, PRDM1A, PRDM1B and EOMES mRNA. Shown are cumulative data of relative fold expression values of cells cultured with CHIR99021 relative to cells cultured with DMSO. All data are normalized against ACTB. B, CD3−CD56+ NK cells from these cultures were also analyzed by intracellular staining and FACS for expression levels of TBX21, ZEB2, BLIMP-1 and EOMES (as determined by mean fluorescence intensity). Shown are cumulative relative fold expression values for each transcription factor in cells cultured with CHIR99021 relative to cells cultured with DMSO. Results are from 2 independent experiments. Data is shown as mean ± SEM, and paired Student’s t tests were used for statistical analyses. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001.

Article Snippet: Flow cytometry Cells were stained with fluorochrome-conjugated antibodies against the following antigens: CD56 (clone HCD56), CD3 (clone OKT3), CD57 (clone NK-1), CD62L (clone DREG-56), CD16 (clone 3G8), CD158a (HP-MA4), CD158b (DX27), NKB1 (DX9), Perforin (dG9), granzyme B (GB11), DNAM-1 (11A8), NKG2D (1D11), NKp80 (5D12), 2B4 (C1.7), TNF (MAb11), IFN-γ (clone B27) (all from Biolegend), NKG2C (134591), BLIMP1 (646702) (from R&D Systems), NKG2A (Z199) (from Beckman Coulter), ZEB2 (from Novus Biologicals), EOMES (WD1928), PLZF (Mags.21F7), SYK (4D10.1) (from eBiosciences), FcεR1γ (from Millipore), and T-BET (04-46) and NKp30 (p30-15) (from BD Pharmingen).

Techniques: Cell Culture, Isolation, Quantitative RT-PCR, Expressing, Staining, Fluorescence

Journal: Cell reports

Article Title: Stromal-induced epithelial-mesenchymal transition induces targetable drug resistance in acute lymphoblastic leukemia

doi: 10.1016/j.celrep.2023.112804

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ZEB2 (E6U7Z) Rabbit mAb , Cell Signaling Technology , Cat# 97885, RRID:AB_2934315.

Techniques: Recombinant, Electron Microscopy, Virus, Derivative Assay, Staining, Cell Viability Assay, Gene Knockout, Activity Assay, Fluorescence, Cell Migration Assay, Transfection, Sequencing, Modification, Control, Software

Journal: Cell

Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

doi: 10.1016/j.cell.2018.08.067

Figure Lengend Snippet: Human Colonic Mesenchymal Heterogeneity in Health (A) Flow cytometry analysis of the indicated surface markers on colonic single-cell suspensions following removal of epithelial and hematopoietic cells by MACS. Column flow-through is shown in red, and column-retained fraction is in blue. (B) t-SNE plot of the healthy human colonic mesenchyme dataset. Single cells colored by cluster annotation. (C) Violin plots for pan-fibroblast marker genes vimentin ( VIM ) and collagen types 1 and 3 ( COL1A2 , COL3A1 ) across clusters. (D) Violin plots for high-ranked transcriptional regulators and marker genes sharing GO annotation for significantly enriched terms for (i) S1 subset, (ii) S2 subset, (iii) S3 subset, (iv) S4 subset, and (v) myofibroblasts. Crossbars indicate median expression. (E) Single-molecule ISH staining of healthy human colonic tissue showing distribution of S1 markers ( ADAMDEC1 , DCN , SLIT2 , and CXCL12 ) (left) and S2 markers ( F3 (CD142) , WNT5A , HSD17B2 , WNT5B , POSTN , BMP2 , FRZB , BMP5 ) (right). (F) Identification of SOX6 − ZEB2 + /ZEB1 − ZEB2 + S1 and SOX6 + ZEB2 − /ZEB1 + ZEB2 − S2 subsets in healthy human colon. (G) Single (left) and co-staining with CD45 (right) and F3/CD142 (S2), ZEB2 (S1), and SMAD7 (S3) by IHC in colonic sections. The lower far-right panel is a quadruple stain of all 4 markers. (H) Differential expression analysis between S2a and S2b reveals 302 differentially expressed genes. (I) t-SNE plots showing examples of genes differentially expressed between S2a and S2b. (J) GO enrichment terms for S2a and S2b. See also – and – .

Article Snippet: Rabbit polyclonal anti-human ZEB2 , Atlas Antibodies , Cat#HPA003456; RRID: AB_10603840.

Techniques: Flow Cytometry, Marker, Expressing, Staining, Quantitative Proteomics

Journal: Cell

Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

doi: 10.1016/j.cell.2018.08.067

Figure Lengend Snippet:

Article Snippet: Rabbit polyclonal anti-human ZEB2 , Atlas Antibodies , Cat#HPA003456; RRID: AB_10603840.

Techniques: Recombinant, Coagulation, Antibody Labeling, Membrane, Plasmid Preparation, Polymer, Blocking Assay, Staining, Imaging, cDNA Synthesis, RNAscope, DNA Library Preparation, Software, Hybridization