mouse 880 anti olig2 Search Results


96
R&D Systems goat anti olig2
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Novus Biologicals anti olig2 rabbit pab
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Proteintech olig2
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Millipore mouse α-olig2
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Merck & Co anti-olig2 antibody
( A ) Scheme to identify EGFP-expressing cell types by fIHC. Neurons and astrocytes were immunolabeled for NeuN and GFAP, respectively. Cells immunostained for <t>Olig2</t> or Iba1 were identified as oligodendrocytes and microglia. Cells were detected with Hoechest 33342, NucBlue, in the mounting reagent ProLong Glass. ( B ) Representative immunohistochemical images of marmoset cerebral cortex that received injection of AAV2. Two serial slices were presented: one immunolabeled for GFP, NeuN, and GFAP, and another one for GFP, Olig2, and Iba1, as indicated at each panel. Scale bar, 100 μm.
Anti Olig2 Antibody, supplied by Merck & Co, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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R&D Systems olig2
( A ) Scheme matching mouse and human neural tube development according to neural patterning and differentiation. ( B-D ) Immunofluorescence in transverse sections of mouse and human neural tubes at shoulder levels from E9.0 to E11.5 in mouse and CS11 to CS17 in human embryos. ( B ) Expression of progenitor markers PAX6 (green), <t>OLIG2</t> (magenta) and NKX2.2 (cyan). ( C ) Pan-neural progenitor marker Sox2 (blue), and motor-neuron markers ISL1 (magenta) and HB9/MNX1 (cyan) at neurogenic stages. ( D ) Early ventral expression of gliogenic markers NFIA (red) and SOX9 (blue) in the neural tube can be detected from E10.5 in mouse and CS15 in human. NFIA also labels neurons, as indicated by TUBB3 (cyan) staining. Scale bars = 50 μm.
Olig2, supplied by R&D Systems, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Cell Signaling Technology Inc anti olig2
(A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as <t>OLIG2</t> positive, and intermediate as positive for both markers.
Anti Olig2, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Merck KGaA anti-olig2 clone 211f1.1 af488 mouse mab
(A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as <t>OLIG2</t> positive, and intermediate as positive for both markers.
Anti Olig2 Clone 211f1.1 Af488 Mouse Mab, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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R&D Systems anti olig2
(A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as <t>OLIG2</t> positive, and intermediate as positive for both markers.
Anti Olig2, supplied by R&D Systems, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Santa Cruz Biotechnology rabbit anti olig2
(A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as <t>OLIG2</t> positive, and intermediate as positive for both markers.
Rabbit Anti Olig2, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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90
Cell Marque anti-olig2
(A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as <t>OLIG2</t> positive, and intermediate as positive for both markers.
Anti Olig2, supplied by Cell Marque, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


( A ) Scheme to identify EGFP-expressing cell types by fIHC. Neurons and astrocytes were immunolabeled for NeuN and GFAP, respectively. Cells immunostained for Olig2 or Iba1 were identified as oligodendrocytes and microglia. Cells were detected with Hoechest 33342, NucBlue, in the mounting reagent ProLong Glass. ( B ) Representative immunohistochemical images of marmoset cerebral cortex that received injection of AAV2. Two serial slices were presented: one immunolabeled for GFP, NeuN, and GFAP, and another one for GFP, Olig2, and Iba1, as indicated at each panel. Scale bar, 100 μm.

Journal: bioRxiv

Article Title: Optimal AAV capsid/promoter combinations to target specific cell types in the common marmoset cerebral cortex

doi: 10.1101/2024.05.09.593444

Figure Lengend Snippet: ( A ) Scheme to identify EGFP-expressing cell types by fIHC. Neurons and astrocytes were immunolabeled for NeuN and GFAP, respectively. Cells immunostained for Olig2 or Iba1 were identified as oligodendrocytes and microglia. Cells were detected with Hoechest 33342, NucBlue, in the mounting reagent ProLong Glass. ( B ) Representative immunohistochemical images of marmoset cerebral cortex that received injection of AAV2. Two serial slices were presented: one immunolabeled for GFP, NeuN, and GFAP, and another one for GFP, Olig2, and Iba1, as indicated at each panel. Scale bar, 100 μm.

Article Snippet: Tissue sections were reacted overnight at room temperature by immersion in following primary antibodies in blocking solution (2% Donkey Serum (S30-100ML, Merck), BSA (01862-87, Nacalai Tesque, Kyoto, Japan), 0.5% Triton X-100, 0.03% NaN3 in 1 x PB): rat monoclonal anti-GFP antibody (1:1,000; 04404-84; Nacalai Tesque, Kyoto, Japan), mouse monoclonal anti-NeuN antibody (1:1,000; MAB377; Merck), rabbit polyclonal anti-GFAP antibody (1:200; GFAP-Rb-Af800; Nittobo Medical, Tokyo, Japan), rabbit polyclonal anti-S-100β antibody (1:200; S100b-Rb-Af1000, Nittobo Medical), mouse monoclonal anti-Olig2 antibody (1:500; MABN50; Merck) and rabbit polyclonal anti-Iba1 antibody (1:500; 019-19741; Fujifilm Wako Chemicals, Tokyo, Japan).

Techniques: Expressing, Immunolabeling, Immunohistochemical staining, Injection

( A ) Schema depicting the AAV genome structure. ( B - C ) Immunolabeled fluorescent images of EGFP in the cerebral cortex that received injection of AAV5 ( B ) or AAVrh10 ( C ) vectors expressing EGFP by the mMBP promoter. The middle immunofluorescence images present an overlay of immunolabeling for EGFP and the oligodendrocyte marker Olig2. The bottom images are magnifications of the boxed areas in the center images. Scale bar, 100 μm. ( D - E ) Summary graphs showing the specificity ( D ) and efficiency ( E ) of oligodendrocyte transduction. The dotted line in the graph indicates a ratio of oligodendrocytes to total cells present in the marmoset cortex (Figure S3). Error bars indicate S.E.M., and dots in the graph indicate the respective values for each of the individual marmosets. Asterisks indicate statistically significant differences between the AAV5 and AAVrh10. ** p < 0.01, *** p < 0.001 by student’s t-test.

Journal: bioRxiv

Article Title: Optimal AAV capsid/promoter combinations to target specific cell types in the common marmoset cerebral cortex

doi: 10.1101/2024.05.09.593444

Figure Lengend Snippet: ( A ) Schema depicting the AAV genome structure. ( B - C ) Immunolabeled fluorescent images of EGFP in the cerebral cortex that received injection of AAV5 ( B ) or AAVrh10 ( C ) vectors expressing EGFP by the mMBP promoter. The middle immunofluorescence images present an overlay of immunolabeling for EGFP and the oligodendrocyte marker Olig2. The bottom images are magnifications of the boxed areas in the center images. Scale bar, 100 μm. ( D - E ) Summary graphs showing the specificity ( D ) and efficiency ( E ) of oligodendrocyte transduction. The dotted line in the graph indicates a ratio of oligodendrocytes to total cells present in the marmoset cortex (Figure S3). Error bars indicate S.E.M., and dots in the graph indicate the respective values for each of the individual marmosets. Asterisks indicate statistically significant differences between the AAV5 and AAVrh10. ** p < 0.01, *** p < 0.001 by student’s t-test.

Article Snippet: Tissue sections were reacted overnight at room temperature by immersion in following primary antibodies in blocking solution (2% Donkey Serum (S30-100ML, Merck), BSA (01862-87, Nacalai Tesque, Kyoto, Japan), 0.5% Triton X-100, 0.03% NaN3 in 1 x PB): rat monoclonal anti-GFP antibody (1:1,000; 04404-84; Nacalai Tesque, Kyoto, Japan), mouse monoclonal anti-NeuN antibody (1:1,000; MAB377; Merck), rabbit polyclonal anti-GFAP antibody (1:200; GFAP-Rb-Af800; Nittobo Medical, Tokyo, Japan), rabbit polyclonal anti-S-100β antibody (1:200; S100b-Rb-Af1000, Nittobo Medical), mouse monoclonal anti-Olig2 antibody (1:500; MABN50; Merck) and rabbit polyclonal anti-Iba1 antibody (1:500; 019-19741; Fujifilm Wako Chemicals, Tokyo, Japan).

Techniques: Immunolabeling, Injection, Expressing, Immunofluorescence, Marker, Transduction

( A ) Scheme matching mouse and human neural tube development according to neural patterning and differentiation. ( B-D ) Immunofluorescence in transverse sections of mouse and human neural tubes at shoulder levels from E9.0 to E11.5 in mouse and CS11 to CS17 in human embryos. ( B ) Expression of progenitor markers PAX6 (green), OLIG2 (magenta) and NKX2.2 (cyan). ( C ) Pan-neural progenitor marker Sox2 (blue), and motor-neuron markers ISL1 (magenta) and HB9/MNX1 (cyan) at neurogenic stages. ( D ) Early ventral expression of gliogenic markers NFIA (red) and SOX9 (blue) in the neural tube can be detected from E10.5 in mouse and CS15 in human. NFIA also labels neurons, as indicated by TUBB3 (cyan) staining. Scale bars = 50 μm.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: ( A ) Scheme matching mouse and human neural tube development according to neural patterning and differentiation. ( B-D ) Immunofluorescence in transverse sections of mouse and human neural tubes at shoulder levels from E9.0 to E11.5 in mouse and CS11 to CS17 in human embryos. ( B ) Expression of progenitor markers PAX6 (green), OLIG2 (magenta) and NKX2.2 (cyan). ( C ) Pan-neural progenitor marker Sox2 (blue), and motor-neuron markers ISL1 (magenta) and HB9/MNX1 (cyan) at neurogenic stages. ( D ) Early ventral expression of gliogenic markers NFIA (red) and SOX9 (blue) in the neural tube can be detected from E10.5 in mouse and CS15 in human. NFIA also labels neurons, as indicated by TUBB3 (cyan) staining. Scale bars = 50 μm.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Immunofluorescence, Expressing, Marker, Staining

(A) Expression of the neuromesodermal progenitor markers SOX2, CDX2, T at day 0 in mouse and human motor neuron differentiations. (B) Percentage of PAX6, NKX6.1 and OLIG2 positive cells at various time points across mouse and human differentiations. (C) Scatter plot with histograms of PAX6 and OLIG2 intensity levels measured by FACS in NPs from mouse cells at day 2 (orange) and human cells at days 4 (dark blue) and day 8 (light blue). (D) PCA plots of RNA-seq data across mouse and human MN differentiation. Shapes of the points indicate biological replicates. (E) Mean scaled expression profiles of selected human and mouse clusters pairs selected that share a higher proportion of homologous genes than expected by chance. (F) Estimated time factor on selected genes measured from the RNAseq dataset. (G) Expression of selected genes in time in mouse (solid orange line) and human differentiations (blue solid line) alognside with the rescaled expression in mouse (dashed orange line) using the estimated time factors for specific genes.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: (A) Expression of the neuromesodermal progenitor markers SOX2, CDX2, T at day 0 in mouse and human motor neuron differentiations. (B) Percentage of PAX6, NKX6.1 and OLIG2 positive cells at various time points across mouse and human differentiations. (C) Scatter plot with histograms of PAX6 and OLIG2 intensity levels measured by FACS in NPs from mouse cells at day 2 (orange) and human cells at days 4 (dark blue) and day 8 (light blue). (D) PCA plots of RNA-seq data across mouse and human MN differentiation. Shapes of the points indicate biological replicates. (E) Mean scaled expression profiles of selected human and mouse clusters pairs selected that share a higher proportion of homologous genes than expected by chance. (F) Estimated time factor on selected genes measured from the RNAseq dataset. (G) Expression of selected genes in time in mouse (solid orange line) and human differentiations (blue solid line) alognside with the rescaled expression in mouse (dashed orange line) using the estimated time factors for specific genes.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Expressing, RNA Sequencing Assay

( A ) Schematic of mouse ESCs differentiated to MNs. Spinal cord progenitors are generated via an NMP state induced by the addition of FGF, WNT and dual SMAD inhibition signals for 24h (blue rectangle), and subsequently exposed to the neuralizing signal retinoic acid (RA) and smoothened agonist (SAG) to ventralise the cells (green). ( B ) Schematic of the analogous strategy used for human ESCs to generate MNs, where the addition of FGF, WNT and dual SMAD inhibition signals lasts 72h. ( C ) Expression of NP markers (PAX6, OLIG2, NKX2.2) between Days 1 and 3 in mouse MN differentiations. ( D ) Expression of NP markers (PAX6, OLIG2, NKX2.2) at Days 4, 6 and 8 in human MN differentiations. ( E ) Expression of MN markers (ISL1, HB9/MNX1) in mouse and human MNs. Mouse MNs can be detected by Days 2-3, whereas human MNs are not detected until days 8 and 10. ( F ) HOXC6 expression in MNs characterized by ISL1 and TUBB3 expression at day 3 in mouse and in human day 10. Scale bars = 50 μm. ( G ) RT-qPCR analysis of Pax6, Olig2, Nkx2.2 and Isl1 expression in mouse and human differentiations reveals a conserved progression in gene expression but a different tempo (human n=9, mouse n=9). ( H ) Heatmap of RNA-seq data across mouse and human MN differentiation indicating the interpolated normalized expression of selected markers representative of neuromesodermal progenitors, neural progenitors, neurons, glia and mesoderm cell types. ( I ) Heatmap of pair wise Pearson correlation coefficients of the transcriptomes of mouse (vertical) and human (horizontal) differentiation at the indicated time points. High positive correlation is indicated by values close to 1 (red). White line shows a linear fit of the Pearson correlation over measuring a temporal scaling factor of 2.5 ± 0.2 (median ± std). ( J ) Scaling factor for transcriptome clusters that contain Pax6, Irx3, Olig2, Nkx2.2, Isl1 and Tubb3. ( K ) Time factor estimations for cluster pairs with high proportion of orthologous genes.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: ( A ) Schematic of mouse ESCs differentiated to MNs. Spinal cord progenitors are generated via an NMP state induced by the addition of FGF, WNT and dual SMAD inhibition signals for 24h (blue rectangle), and subsequently exposed to the neuralizing signal retinoic acid (RA) and smoothened agonist (SAG) to ventralise the cells (green). ( B ) Schematic of the analogous strategy used for human ESCs to generate MNs, where the addition of FGF, WNT and dual SMAD inhibition signals lasts 72h. ( C ) Expression of NP markers (PAX6, OLIG2, NKX2.2) between Days 1 and 3 in mouse MN differentiations. ( D ) Expression of NP markers (PAX6, OLIG2, NKX2.2) at Days 4, 6 and 8 in human MN differentiations. ( E ) Expression of MN markers (ISL1, HB9/MNX1) in mouse and human MNs. Mouse MNs can be detected by Days 2-3, whereas human MNs are not detected until days 8 and 10. ( F ) HOXC6 expression in MNs characterized by ISL1 and TUBB3 expression at day 3 in mouse and in human day 10. Scale bars = 50 μm. ( G ) RT-qPCR analysis of Pax6, Olig2, Nkx2.2 and Isl1 expression in mouse and human differentiations reveals a conserved progression in gene expression but a different tempo (human n=9, mouse n=9). ( H ) Heatmap of RNA-seq data across mouse and human MN differentiation indicating the interpolated normalized expression of selected markers representative of neuromesodermal progenitors, neural progenitors, neurons, glia and mesoderm cell types. ( I ) Heatmap of pair wise Pearson correlation coefficients of the transcriptomes of mouse (vertical) and human (horizontal) differentiation at the indicated time points. High positive correlation is indicated by values close to 1 (red). White line shows a linear fit of the Pearson correlation over measuring a temporal scaling factor of 2.5 ± 0.2 (median ± std). ( J ) Scaling factor for transcriptome clusters that contain Pax6, Irx3, Olig2, Nkx2.2, Isl1 and Tubb3. ( K ) Time factor estimations for cluster pairs with high proportion of orthologous genes.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Generated, Inhibition, Expressing, Quantitative RT-PCR, RNA Sequencing Assay

( A ) Scatter plot with histograms of PAX6 and NKX6.1 expression measured by FACS in neural progenitors from wt (orange) and hChr21 containing (purple) mouse cells at day 2. ( B ) RT-qPCR analysis for the NP and neuronal markers Pax6, Nkx6.1, Nkx2.2 and Isl1 in wt and hChr21 lines. ( C ) RT-qPCR expression of Olig2 from the mouse (mOlig2) and human alleles (hOlig2) in wt and hChr21 lines. ( D ) smFISH at day 2 of differentiation in wt and hChr21 lines with probes for mSox2, and allele specific detection of mOlig2 or human Olig2 (hOLIG2). Scale bars = 10μm ( E ) Boxplots of RNA molecules per cell in wt and hChr21 cells using Sox2, Olig2 and human- and mouse-allele specific probes. ( F ) smFISH in human NPs at day 8 of differentiation for hSOX2 and hOLIG2. Scale bars = 50μm. ( G ) Boxplots of Sox2 and Olig2 mRNA molecules per cell in human NPs at day 8 and mouse wt and hChr21 cells at day 2.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: ( A ) Scatter plot with histograms of PAX6 and NKX6.1 expression measured by FACS in neural progenitors from wt (orange) and hChr21 containing (purple) mouse cells at day 2. ( B ) RT-qPCR analysis for the NP and neuronal markers Pax6, Nkx6.1, Nkx2.2 and Isl1 in wt and hChr21 lines. ( C ) RT-qPCR expression of Olig2 from the mouse (mOlig2) and human alleles (hOlig2) in wt and hChr21 lines. ( D ) smFISH at day 2 of differentiation in wt and hChr21 lines with probes for mSox2, and allele specific detection of mOlig2 or human Olig2 (hOLIG2). Scale bars = 10μm ( E ) Boxplots of RNA molecules per cell in wt and hChr21 cells using Sox2, Olig2 and human- and mouse-allele specific probes. ( F ) smFISH in human NPs at day 8 of differentiation for hSOX2 and hOLIG2. Scale bars = 50μm. ( G ) Boxplots of Sox2 and Olig2 mRNA molecules per cell in human NPs at day 8 and mouse wt and hChr21 cells at day 2.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Expressing, Quantitative RT-PCR

(A) Expression of Sod1 and Son human genes located on Chromosome 21, the neural markers Tubb3 and Olig 1 and the mesoderm marker Meoxl in wt and hChr21 differentiations. (B) Percentage of OLIG2 positive cells from days 0 to 4 in wt and hChr21 differentiation show no major changes in cell proportions over time. (C) Representative images of smFISH used for segmentation and quantification of wt and hChr21 mouse cells. (D) Representative images of smFISH used for segmentation and quantification of human MN differentiation. (E) Sox2 and total Olig2 mRNA number in human, wt and hChr21 neural progenitors. (F) hSOX2 and hOLIG2 mRNA number in human neural progenitors at days 4, 5 and 6. Scale bars 50μM.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: (A) Expression of Sod1 and Son human genes located on Chromosome 21, the neural markers Tubb3 and Olig 1 and the mesoderm marker Meoxl in wt and hChr21 differentiations. (B) Percentage of OLIG2 positive cells from days 0 to 4 in wt and hChr21 differentiation show no major changes in cell proportions over time. (C) Representative images of smFISH used for segmentation and quantification of wt and hChr21 mouse cells. (D) Representative images of smFISH used for segmentation and quantification of human MN differentiation. (E) Sox2 and total Olig2 mRNA number in human, wt and hChr21 neural progenitors. (F) hSOX2 and hOLIG2 mRNA number in human neural progenitors at days 4, 5 and 6. Scale bars 50μM.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Expressing, Marker

(A) Schematic of EU experiment to measure RNA half-lives in mouse and human neural progenitors. Cells are cultured for 3h with the uriridine analog EU (green). A sample that contains maximal levels of EU incorpotation is collected (pulse). Subsequently, EU is removed and cells are collected at various time points. (B) Representative histograms of EU incorporation intensity measurements to estimate mRNA half-life from mouse day 2 (orange) and human day 4 (blue) neural progenitors. (C) Schematic of AHA experiment to measure protein half-lives in mouse and human neural progenitors. Cells are grown on methionine-free media for 45h and then cultured for 2h with the methionine analog AHA (green). A sample that contains maximal levels of AHA incorpotation is collected (pulse). Subsequently, AHA is removed and cells are collected at various time points. (D) Representative histograms of AHA incorporation intensity measurements to estimate protein half-life from mouse day 2 (orange) and human day 8 (blue) neural progenitors. (E) Normalized RT-qPCR analysis of RNA enrichment relative to Actin of EU-nascent RNA captured on magenetic beads after pulse and chase experiments. (F) Estimated time factor as a function of the degradation rate ratio accros various dorsoventral (DV) positions. (G) Representative mouse (G) and human (H) detection of NKX6.1, OLIG2, S0X1 and SOX2 after AHA pulse-chase experiments on nascent proteins.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: (A) Schematic of EU experiment to measure RNA half-lives in mouse and human neural progenitors. Cells are cultured for 3h with the uriridine analog EU (green). A sample that contains maximal levels of EU incorpotation is collected (pulse). Subsequently, EU is removed and cells are collected at various time points. (B) Representative histograms of EU incorporation intensity measurements to estimate mRNA half-life from mouse day 2 (orange) and human day 4 (blue) neural progenitors. (C) Schematic of AHA experiment to measure protein half-lives in mouse and human neural progenitors. Cells are grown on methionine-free media for 45h and then cultured for 2h with the methionine analog AHA (green). A sample that contains maximal levels of AHA incorpotation is collected (pulse). Subsequently, AHA is removed and cells are collected at various time points. (D) Representative histograms of AHA incorporation intensity measurements to estimate protein half-life from mouse day 2 (orange) and human day 8 (blue) neural progenitors. (E) Normalized RT-qPCR analysis of RNA enrichment relative to Actin of EU-nascent RNA captured on magenetic beads after pulse and chase experiments. (F) Estimated time factor as a function of the degradation rate ratio accros various dorsoventral (DV) positions. (G) Representative mouse (G) and human (H) detection of NKX6.1, OLIG2, S0X1 and SOX2 after AHA pulse-chase experiments on nascent proteins.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Cell Culture, Quantitative RT-PCR, Pulse Chase

( A ) Normalized EU incorporation intensity measurements to estimate mRNA half-life in mouse (orange) and human (blue) neural progenitors. Line and shadowed areas show best exponential fit and its 70% High Density Interval (HDI). (B) Half-life of the transcriptome in mouse neural progenitors at day two (orange), and human neural progenitors at day 4 (dark blue) and day 8 (light blue). ( C ) Normalized AHA intensity measurements of the proteome in mouse (orange) and human (blue) neural progenitors to estimate protein stability. (D) Global stability of the proteome in mouse neural progenitors at day two (orange), and human neural progenitors at days 4 (dark blue) and day 8 (light blue). Statistical significance (**) corresponds with <1% of overlap between the distributions of parameter estimations. (E) Diagram of the cross-repressive GRN comprising the TFs Pax6, Olig2, Nkx2,2 and Irx3 used to model ventral patterning of the neural tube. (F) Temporal dynamics of the simulated GRN model at a relative dorsoventral (DV) position x=0.2 for the mouse model, and the predicted human behaviour by halving the degradation rates of the proteins of the network. (G) Estimated time factor at a DV position x=0.2 plotted as a function of the fold change in the degradation rate ratio (blue solid line). The dashed line corresponds to the linear relationship where the degradation rate is the same as the time factor.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: ( A ) Normalized EU incorporation intensity measurements to estimate mRNA half-life in mouse (orange) and human (blue) neural progenitors. Line and shadowed areas show best exponential fit and its 70% High Density Interval (HDI). (B) Half-life of the transcriptome in mouse neural progenitors at day two (orange), and human neural progenitors at day 4 (dark blue) and day 8 (light blue). ( C ) Normalized AHA intensity measurements of the proteome in mouse (orange) and human (blue) neural progenitors to estimate protein stability. (D) Global stability of the proteome in mouse neural progenitors at day two (orange), and human neural progenitors at days 4 (dark blue) and day 8 (light blue). Statistical significance (**) corresponds with <1% of overlap between the distributions of parameter estimations. (E) Diagram of the cross-repressive GRN comprising the TFs Pax6, Olig2, Nkx2,2 and Irx3 used to model ventral patterning of the neural tube. (F) Temporal dynamics of the simulated GRN model at a relative dorsoventral (DV) position x=0.2 for the mouse model, and the predicted human behaviour by halving the degradation rates of the proteins of the network. (G) Estimated time factor at a DV position x=0.2 plotted as a function of the fold change in the degradation rate ratio (blue solid line). The dashed line corresponds to the linear relationship where the degradation rate is the same as the time factor.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques:

(A) Mouse and human normalized intensity measurements of NKX6.1, OLIG2, SOX1 and SOX2 after AHA pulse-chase experiments on AHA-labeled and purified nascent proteins. Line and shadowed areas show best exponential fit with 95% confidence intervals. (B) Normalized intensity measurements of mKATE2 in mouse and human Ptch1::T2A-mKate2 cell lines. Line and shadowed areas show best exponential fit and its 70% HDI. (C) Estimated half-lives for mKATE2 in mouse (orange) and human (blue) cells. (D) Cell cycle measurements of mouse neural progenitors at day two, and human neural progenitors at days 4 and 8. Line and shadowed areas show best fit and its 80% HDI (E) Cell cycle length estimations in mouse neural progenitors at day two, and human neural progenitors at days 4 and 8. For all plots, mouse data is orange-colored, and human is blue. Statistical significance (**) corresponds with <1% of overlap between the distributions of parameter estimations.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: (A) Mouse and human normalized intensity measurements of NKX6.1, OLIG2, SOX1 and SOX2 after AHA pulse-chase experiments on AHA-labeled and purified nascent proteins. Line and shadowed areas show best exponential fit with 95% confidence intervals. (B) Normalized intensity measurements of mKATE2 in mouse and human Ptch1::T2A-mKate2 cell lines. Line and shadowed areas show best exponential fit and its 70% HDI. (C) Estimated half-lives for mKATE2 in mouse (orange) and human (blue) cells. (D) Cell cycle measurements of mouse neural progenitors at day two, and human neural progenitors at days 4 and 8. Line and shadowed areas show best fit and its 80% HDI (E) Cell cycle length estimations in mouse neural progenitors at day two, and human neural progenitors at days 4 and 8. For all plots, mouse data is orange-colored, and human is blue. Statistical significance (**) corresponds with <1% of overlap between the distributions of parameter estimations.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Pulse Chase, Labeling, Purification

(A) RT-qPCR analysis of Pax6, Olig2, Nkx2.2 and Isl1 expression in mouse and human differentiations from the Ptchl-mKATE2 targeted stem cell lines. (B) Representative histograms of mKATE2 intensity measurements to estimate protein half-life from mouse (orange) and human (blue) neural progenitors. (C) Representatve histograms of DNA content of mouse and human cells, and dual parameter plots of Alexa Fluor 488-conjugated EdU and DNA indicating the gates to quantify EdU positive cells. (D) Pairwise relationships between proportion of S phase estimations (c 0 ), cell cycle lenght ( T ) and saturation (σ) in mouse and human cells.

Journal: bioRxiv

Article Title: Species-specific developmental timing is associated with global differences in protein stability in mouse and human

doi: 10.1101/2019.12.29.889543

Figure Lengend Snippet: (A) RT-qPCR analysis of Pax6, Olig2, Nkx2.2 and Isl1 expression in mouse and human differentiations from the Ptchl-mKATE2 targeted stem cell lines. (B) Representative histograms of mKATE2 intensity measurements to estimate protein half-life from mouse (orange) and human (blue) neural progenitors. (C) Representatve histograms of DNA content of mouse and human cells, and dual parameter plots of Alexa Fluor 488-conjugated EdU and DNA indicating the gates to quantify EdU positive cells. (D) Pairwise relationships between proportion of S phase estimations (c 0 ), cell cycle lenght ( T ) and saturation (σ) in mouse and human cells.

Article Snippet: Primary antibodies were diluted as follows: rabbit anti-Pax6 (Covance 1:500), goat-anti Olig2 (R&D AF2418, 1:800), mouse anti-Nkx2.2 (,1:500), mouse anti-Hb9/Mnx1 (DSHB, 1:40), goat anti-Isl1 (R&D AF1837, 1:1,000), mouse anti-Hoxc6 (Santa Cruz Biotechnology sc-376330, 1:200), mouse anti-Tubb3 (Covance MMS-435P, 1:500), chicken anti-Tubb3 (Abcam ab107216, 1:500), goat anti-sox2 (R&D, 1:500), goat anti-sox9 (R&D AF3075, 1:250), rabbit anti-NFIA (Atlas antibodies HPA008884, 1:500).

Techniques: Quantitative RT-PCR, Expressing

(A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as OLIG2 positive, and intermediate as positive for both markers.

Journal: bioRxiv

Article Title: Spatial epigenomic niches underlie glioblastoma cell state plasticity

doi: 10.1101/2025.05.09.653178

Figure Lengend Snippet: (A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as OLIG2 positive, and intermediate as positive for both markers.

Article Snippet: Primary antibody staining was performed overnight at 4 °C using anti-OLIG2 (Cell Signaling, 65915) diluted 1:400 in DPBS supplemented with 1% Bovine Serum Albumin (BSA) and 0.3% Triton™ X-100 (pH 8.0).

Techniques: Activity Assay, Microscopy

(A) Schematic demonstrating how data are portrayed for panels B and C. (B – C) Signaling programs as defined by NicheCompass demonstrating PDGFB signaling within the OPC-like niche and GPI signaling from the MES-like niche to the OPC-like niche. (D) Heatmap of signaling probabilities as defined by CellChat based on snATAC data of malignant GBM cells. (E) Top ligand-receptor pairs contributing to BMP signaling pathway. (F) Violin plots of BMP7 expression in single cell RNA sequencing data from Couturier and colleagues. (G) Violin plot of gene activity score from snATAC dataset. Note the relatively modest difference in gene activity. (H) Coverage plot of the BMP7 gene. Note relatively similar chromatin landscape. (I) Fluorescence microscopy images of GBM cell culture (GSC016) under control conditions and after treatment for 72 hours with recombinant BMP7 (n = 2 – 4 wells per condition). Scale bar indicates 100 µm. (J) Quantification of percent OLIG2 positive cells in (I).

Journal: bioRxiv

Article Title: Spatial epigenomic niches underlie glioblastoma cell state plasticity

doi: 10.1101/2025.05.09.653178

Figure Lengend Snippet: (A) Schematic demonstrating how data are portrayed for panels B and C. (B – C) Signaling programs as defined by NicheCompass demonstrating PDGFB signaling within the OPC-like niche and GPI signaling from the MES-like niche to the OPC-like niche. (D) Heatmap of signaling probabilities as defined by CellChat based on snATAC data of malignant GBM cells. (E) Top ligand-receptor pairs contributing to BMP signaling pathway. (F) Violin plots of BMP7 expression in single cell RNA sequencing data from Couturier and colleagues. (G) Violin plot of gene activity score from snATAC dataset. Note the relatively modest difference in gene activity. (H) Coverage plot of the BMP7 gene. Note relatively similar chromatin landscape. (I) Fluorescence microscopy images of GBM cell culture (GSC016) under control conditions and after treatment for 72 hours with recombinant BMP7 (n = 2 – 4 wells per condition). Scale bar indicates 100 µm. (J) Quantification of percent OLIG2 positive cells in (I).

Article Snippet: Primary antibody staining was performed overnight at 4 °C using anti-OLIG2 (Cell Signaling, 65915) diluted 1:400 in DPBS supplemented with 1% Bovine Serum Albumin (BSA) and 0.3% Triton™ X-100 (pH 8.0).

Techniques: Expressing, RNA Sequencing, Activity Assay, Fluorescence, Microscopy, Cell Culture, Control, Recombinant