Journal: Biology Open

Article Title: In vivo genetic manipulation of cortical progenitors in gyrencephalic carnivores using in utero electroporation

doi: 10.1242/bio.20123160

Figure Lengend Snippet: In utero electroporation was performed at E37, and sections were prepared at E40. The sections were immunostained with anti-Sox2, anti-Pax6 and anti-Tbr2 antibodies. The cerebral cortex is shown in A . The areas within the white boxes are magnified and are shown in B . CP, cortical plate; OSVZ, outer subventricular zone; ISVZ, inner subventricular zone; VZ, ventricular zone. Scale bars: 200 µm (A) and 100 µm (B).

Article Snippet: Sections were made using a cryostat, permeabilized with 0.1–0.5% Triton X-100/PBS, and incubated overnight with primary antibodies, which included anti-Sox2 antibody (R&D Systems), anti-Pax6 antibody (Covance), anti-Tbr2 antibody (Abcam) and anti-neurofilament-M antibody (Chemicon).

Techniques: In Utero, Electroporation

Journal: Biology Open

Article Title: In vivo genetic manipulation of cortical progenitors in gyrencephalic carnivores using in utero electroporation

doi: 10.1242/bio.20123160

Figure Lengend Snippet: In utero electroporation was performed at E35, and coronal sections were prepared at P0 and were stained with Hoechst 33342. Many GFP-positive cells were distributed throughout the cortex ( A ). The areas within the white boxes in A are magnified and are shown in B . The areas within the white boxes in B are shown in C . Note that the morphology of GFP-positive cells was clearly visible even without immunostaining. ( D , E ) The sections were immunostained with anti-Sox2 antibody (D) and anti-Pax6 antibody (E), and high magnification images of the OSVZ are shown. The GFP-positive cells (arrowheads) expressed Sox2 (D) and Pax6 (E), and had basal fibers but not apical fibers, suggesting that these cell are oRG cells. GFP-positive fibers running tangentially in the inner OSVZ were also visible (arrow). *Lateral ventricle. CP, cortical plate; OSVZ, outer subventricular zone; ISVZ, inner subventricular zone; VZ, ventricular zone. Scale bars: 1 mm (A), 500 µm (B), 100 µm (C) and 20 µm (D,E).

Article Snippet: Sections were made using a cryostat, permeabilized with 0.1–0.5% Triton X-100/PBS, and incubated overnight with primary antibodies, which included anti-Sox2 antibody (R&D Systems), anti-Pax6 antibody (Covance), anti-Tbr2 antibody (Abcam) and anti-neurofilament-M antibody (Chemicon).

Techniques: In Utero, Electroporation, Staining, Immunostaining

Journal: Cancer Research

Article Title: Down-Regulation of Stem Cell Genes, Including Those in a 200-kb Gene Cluster at 12p13.31, Is Associated withIn vivoDifferentiation of Human Male Germ Cell Tumors

doi: 10.1158/0008-5472.can-05-2445

Figure Lengend Snippet: Figure 4. Immunohistochemical analysis of SOX2 expression in embryonal carcinoma, seminoma, and ITGCN. Nuclear SOX2 staining in (A) ITGCN, (B) seminoma, and (C) embryonal carcinoma.

Article Snippet: SOX2 antibody (R&D Systems, Minneapolis, MN; diluted 1:100) was incubated on the section overnight at 4jC.

Techniques: Immunohistochemical staining, Expressing, Staining

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: Super-enhancer profiling identifies a novel subtype of LUSC. A, Unsupervised hierarchical clustering of 13 LUSC cell lines using super-enhancer (SE) signals near transcriptional regulator genes. SE signals were normalized to linear scores using the sum of squares of the values with GenePatten. Duplicate data are shown for LK2 and NCI-H520 cells. B, Copy number of SOX2 and mRNA expression of SOX2, TP63 and POU3F2 in LUSC cell lines from CCLE. C, Super-enhancer plots using H3K27ac scores in the small subset of LUSC cell lines; LK2 cells (left) and NCI-H520 cells (right). D, Genome view tracks of H3K27ac signal at loci of SOX2 (left), TP63 (middle) and POU3F2 (right) in LUSC cell lines. Normalized signals are shown in a range from 0 to 50 for all the tracks. E, Protein expression of Brn2, p63, Sox2 and vinculin as a loading control in LUSC cell lines.

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Expressing

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: Brn2 is expressed in a subset of human primary LUSC tumors. A, Expression of POU3F2 in 501 TCGA LUSC tumor tissues. The red dashed line (TPM=1) shows the cutoff to separate samples into POU3F2 high and low samples. B, Box plots of POU3F2 expression in TP63 high and low LUSC tumors from TCGA, SCLC tumors from publicly available datasets and normal brain tissues (hypothalamus) from GTEx. C, Immunohistochemical staining of Brn2 and Sox2 and H&E staining in Brn2-positive and negative human LUSC tumors. Representative images are shown (original images, ×400). D, Scatter plots of expression of SOX2 and POU3F2 in TP63-low LUSC tumors from TCGA.

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Expressing, Immunohistochemical staining, Staining

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: Brn2 and Sox2 interact and co-localize at genetic loci in the ‘neural’ subset of LUSC. A, Expression of endogenous Brn2 and Sox2 in LK2 cells, determined by immunofluorescence with anti-Sox2 (green) and anti-Brn2 (red) antibodies, respectively. DAPI staining (nuclei; blue) and merged images are also shown. Original magnification, ×200. Scale bar, 100 μm. B, Sox2-Brn2 interaction, shown by co-immunoprecipitation of Sox2 using an antibody against endogenous Brn2 (top) and co-immunoprecipitation of Brn2 using an antibody against endogenous Sox2 (bottom) in LK2 and NCI-H520 cells. C, Heatmap depicting global analysis of ChIP-seq signals for Brn2 and Sox2 in ‘neural’ NCI-H520 and LK2 cells and those for Sox2 in ‘classical’ HCC95, KNS62 and HCC2814 cells at all the peak loci. ChIP-seq signal intensity is shown by color shading. D, Genome view tracks of Brn2, Sox2 and H3K27ac ChIP-seq signals in NCI-H520 and LK2 cells, and Sox2 and H3K27ac ChIP signals in HCC95, KNS62 and HCC2814 cells at loci of POU3F2 (left) and TP63 (right).

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Expressing, Immunofluorescence, Staining, Immunoprecipitation, ChIP-sequencing

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: DNp63 overexpression in the ‘neural’ LUSC cells suppresses Brn2 expression and induces phenotypic changes. A, Protein expression of p63, Brn2, Sox2 and vinculin as a loading control in parental, GFP-overexpressed and DNp63-overexpressed LK2 cells. B, Phase-contrast microphotographs of GFP-overexpressed and DNp63-overexpressed LK2 cells. Bar = 100 μm. C, Cell growth of GFP-overexpressed and DNp63-overexpressed LK2 cells. Mean ± SD of sextuplicates are shown. **, P<0.001 vs. GFP-overexpressed LK2 cells, t-test. D, Tumor growth of GFP-overexpressed and DNp63-overexpressed LK2 cells in vivo. Mean ± SD of tetraplicates are shown. **, P<0.001 vs. GFP-overexpressed xenografts, t-test. Xenograft tumors resected 19 days after inoculation are shown in the right picture. E, H&E staining and immunohistochemical staining of Brn2 and p63 in GFP-overexpressed or DNp63-overexpressed LK2 xenograft. Original Images, ×400.

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Over Expression, Expressing, In Vivo, Staining, Immunohistochemical staining

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: DNp63 induces a classical squamous-cell transcriptional program in the ‘neural’ LUSC cells. A, Heatmap showing 399 differentially expressed genes (287 up-regulated and 112 down-regulated genes) between control LK2 cells (stable GFP-overexpressed cells and doxycycline-inducible DNp63-overexpressing cells without doxycycline in duplicate) and DNp63-overexpressed LK2 cells (stable DNp63-overexpressed cells and doxycycline-inducible DNp63-overexpressing cells with 2 μg/ml doxycycline in duplicate), sorted by fold change. Color scheme represents Z-score distribution. B, Gene ontology analyses for the differentially up-regulated (top) and down-regulated (bottom) genes upon DNp63 overexpression in LK2 cells. Enriched functions for these genes are identified based on Fisher’s exact test against GO terms curated in MSigDB. C, Average ChIP-seq signals for all Sox2 peaks (top) and Sox2 peaks exclusively found in ‘classical’ HCC95, KNS62 and HCC2814 cells (bottom) in GFP-overexpressed and DNp63-overexpressed LK2 cells. D, Genome view tracks of Sox2 ChIP-seq signals in GFP-overexpressed and DNp63-overexpressed LK2 cells, HCC95, KNS62 and HCC2814 cells and p63 ChIP signals in DNp63-overexpressed LK2 cells and HCC95 cells at loci of TP63 (top) and CTDSPL (bottom).

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Over Expression, ChIP-sequencing

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: Super-enhancer profiling identifies a novel subtype of LUSC. A, Unsupervised hierarchical clustering of 13 LUSC cell lines using super-enhancer (SE) signals near transcriptional regulator genes. SE signals were normalized to linear scores using the sum of squares of the values with GenePatten. Duplicate data are shown for LK2 and NCI-H520 cells. B, Copy number of SOX2 and mRNA expression of SOX2, TP63 and POU3F2 in LUSC cell lines from CCLE. C, Super-enhancer plots using H3K27ac scores in the small subset of LUSC cell lines; LK2 cells (left) and NCI-H520 cells (right). D, Genome view tracks of H3K27ac signal at loci of SOX2 (left), TP63 (middle) and POU3F2 (right) in LUSC cell lines. Normalized signals are shown in a range from 0 to 50 for all the tracks. E, Protein expression of Brn2, p63, Sox2 and vinculin as a loading control in LUSC cell lines.

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Expressing

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: Brn2 is expressed in a subset of human primary LUSC tumors. A, Expression of POU3F2 in 501 TCGA LUSC tumor tissues. The red dashed line (TPM=1) shows the cutoff to separate samples into POU3F2 high and low samples. B, Box plots of POU3F2 expression in TP63 high and low LUSC tumors from TCGA, SCLC tumors from publicly available datasets and normal brain tissues (hypothalamus) from GTEx. C, Immunohistochemical staining of Brn2 and Sox2 and H&E staining in Brn2-positive and negative human LUSC tumors. Representative images are shown (original images, ×400). D, Scatter plots of expression of SOX2 and POU3F2 in TP63-low LUSC tumors from TCGA.

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Expressing, Immunohistochemical staining, Staining

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: Brn2 and Sox2 interact and co-localize at genetic loci in the ‘neural’ subset of LUSC. A, Expression of endogenous Brn2 and Sox2 in LK2 cells, determined by immunofluorescence with anti-Sox2 (green) and anti-Brn2 (red) antibodies, respectively. DAPI staining (nuclei; blue) and merged images are also shown. Original magnification, ×200. Scale bar, 100 μm. B, Sox2-Brn2 interaction, shown by co-immunoprecipitation of Sox2 using an antibody against endogenous Brn2 (top) and co-immunoprecipitation of Brn2 using an antibody against endogenous Sox2 (bottom) in LK2 and NCI-H520 cells. C, Heatmap depicting global analysis of ChIP-seq signals for Brn2 and Sox2 in ‘neural’ NCI-H520 and LK2 cells and those for Sox2 in ‘classical’ HCC95, KNS62 and HCC2814 cells at all the peak loci. ChIP-seq signal intensity is shown by color shading. D, Genome view tracks of Brn2, Sox2 and H3K27ac ChIP-seq signals in NCI-H520 and LK2 cells, and Sox2 and H3K27ac ChIP signals in HCC95, KNS62 and HCC2814 cells at loci of POU3F2 (left) and TP63 (right).

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Expressing, Immunofluorescence, Staining, Immunoprecipitation, ChIP-sequencing

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: DNp63 overexpression in the ‘neural’ LUSC cells suppresses Brn2 expression and induces phenotypic changes. A, Protein expression of p63, Brn2, Sox2 and vinculin as a loading control in parental, GFP-overexpressed and DNp63-overexpressed LK2 cells. B, Phase-contrast microphotographs of GFP-overexpressed and DNp63-overexpressed LK2 cells. Bar = 100 μm. C, Cell growth of GFP-overexpressed and DNp63-overexpressed LK2 cells. Mean ± SD of sextuplicates are shown. **, P<0.001 vs. GFP-overexpressed LK2 cells, t-test. D, Tumor growth of GFP-overexpressed and DNp63-overexpressed LK2 cells in vivo. Mean ± SD of tetraplicates are shown. **, P<0.001 vs. GFP-overexpressed xenografts, t-test. Xenograft tumors resected 19 days after inoculation are shown in the right picture. E, H&E staining and immunohistochemical staining of Brn2 and p63 in GFP-overexpressed or DNp63-overexpressed LK2 xenograft. Original Images, ×400.

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Over Expression, Expressing, In Vivo, Staining, Immunohistochemical staining

Journal: Cancer research

Article Title: Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma

doi: 10.1158/0008-5472.CAN-19-2132

Figure Lengend Snippet: DNp63 induces a classical squamous-cell transcriptional program in the ‘neural’ LUSC cells. A, Heatmap showing 399 differentially expressed genes (287 up-regulated and 112 down-regulated genes) between control LK2 cells (stable GFP-overexpressed cells and doxycycline-inducible DNp63-overexpressing cells without doxycycline in duplicate) and DNp63-overexpressed LK2 cells (stable DNp63-overexpressed cells and doxycycline-inducible DNp63-overexpressing cells with 2 μg/ml doxycycline in duplicate), sorted by fold change. Color scheme represents Z-score distribution. B, Gene ontology analyses for the differentially up-regulated (top) and down-regulated (bottom) genes upon DNp63 overexpression in LK2 cells. Enriched functions for these genes are identified based on Fisher’s exact test against GO terms curated in MSigDB. C, Average ChIP-seq signals for all Sox2 peaks (top) and Sox2 peaks exclusively found in ‘classical’ HCC95, KNS62 and HCC2814 cells (bottom) in GFP-overexpressed and DNp63-overexpressed LK2 cells. D, Genome view tracks of Sox2 ChIP-seq signals in GFP-overexpressed and DNp63-overexpressed LK2 cells, HCC95, KNS62 and HCC2814 cells and p63 ChIP signals in DNp63-overexpressed LK2 cells and HCC95 cells at loci of TP63 (top) and CTDSPL (bottom).

Article Snippet: After centrifugation to remove insoluble debris, lysates were immunoblotted with use of an anti-Brn2 antibody (Santa Cruz Biotechnology, sc-393324 or Cell Signaling Technology, #12137), anti-p63 antibody (Santa Cruz Biotechnology, sc-8344, sc-8431 or Cell Signaling Technology, #13109), anti-Sox2 antibody (R&D, AF2018 or Cell Signaling Technology, #3579), anti-ErbB4 antibody (Cell Signaling Technology, #4795), anti-phospho-ErbB4 antibody (Cell Signaling Technology, #4757), anti-ErbB3 antibody (Cell Signaling Technology, #12708), anti-phospho-ErbB3 antibody (Cell Signaling Technology, #4791), anti-EGFR antibody (Millipore, #06-847), anti-phospho-EGFR antibody (Abcam, ab40815) anti-phospho-Akt antibody (Cell Signaling Technology, #4060) and anti-phospho-Erk1/2 antibody (Cell Signaling Technology, #4370), anti-Ascl1 antibody (Santa Cruz, sc-374104), anti-SYP antibody (Santa Cruz, sc-17750), anti-β-Actin antibody (Sigma), or anti-vinculin (Sigma).

Techniques: Over Expression, ChIP-sequencing

Journal: PLoS ONE

Article Title: Angiogenesis in the Developing Spinal Cord: Blood Vessel Exclusion from Neural Progenitor Region Is Mediated by VEGF and Its Antagonists

doi: 10.1371/journal.pone.0116119

Figure Lengend Snippet: (A) A transverse section of highlighter ink-infused spinal cord was co-stained with the progenitor marker Sox2. (B-E) Sections were stained for markers for differentiated zone, HuC/D, Tuj-1, NF, and HA. For A, B, and E, and 100 μm thick section was processed with confocal microscopy. Sections shown in C and D were 10 μm thick photographed by the conventional fluorescent microscope (Apotome-processed). (F) Growing INVP (arrows) stained with αSMA was located by the NeuroM -positive zone revealed by section in situ hybridization. F’ is a magnified view of the square in F. conf: a confocal image obtained by Z-stack for 70 μm out of 100 μm histological section. Arrows: growing vdINVP. (A, B) E4.5/HH24. (C-F) E5/HH26. Scale bars: 100 μm.

Article Snippet: After washing in PBS containing 0.5% Triton X-100 and blocking with 2% skim milk/PBST (PBS containing 0.1% Tween 20) for 2 h at RT, the sections were incubated overnight at 4°C with diluted antibodies in 2% skim milk/PBST; 1:50 of anti-Sox2 goat polyclonal antibody (R&D systems), 1:100 of anti-HuC/D mouse monoclonal antibody (Molecular Probes), 1:300 of anti-β-tublin III (Tuj-1) mouse monoclonal antibody (R&D systems).

Techniques: Staining, Marker, Confocal Microscopy, Microscopy, In Situ Hybridization