Journal:

Article Title: Brain Lipid Binding Protein in Axon-Schwann Cell Interactions and Peripheral Nerve Tumorigenesis

doi: 10.1128/MCB.23.6.2213-2224.2003

Figure Lengend Snippet: mRNA expression analysis in Nf1 mutant mouse Schwann cells. (A) Microarray analysis was used to compare genome-wide expression levels between normal mouse Schwann cells and Nf1 mutant Schwann cells. The control for each comparison was Cy3-labeled cDNA generated from normal mouse Schwann cell mRNA. For each of four Nf1 mutant Schwann cell samples (Nf1+/−, Nf1−/−, Nf1−/− TXF, and Nf1−/− TXF treated with FTI), mRNA was used as a template to synthesize Cy5-labeled cDNA. Cy3- and Cy5-labeled cDNA probes were hybridized simultaneously to the Incyte Genomics MouseGEM 1.0 cDNA microarray. Relative intensities of Cy3 versus Cy5 fluorescent signals for each cDNA target sequence were analyzed with GeneSpring software. The most changes were observed in the Nf1−/− TXF cells (genes upregulated in Nf1−/− TXF are red; genes downregulated in Nf1−/− TXF are green). Expression of one target cDNA, BLBP (black line), was 26-fold above normal in the Nf1−/− TXF cells and not normalized by FTI treatment. (B) RT-PCR analysis confirmedthe microarray result of elevated BLBP expression in Nf1−/− TXF cells. Reverse transcriptase (RT) was omitted from duplicate samples to control for DNA contamination. Primers for BLBP (∼200-bp amplicon) and actin control primers (∼500-bp amplicon) were included in the mixture for each 40-cycle reaction. The plasmid positive control for BLBP amplification is the UniGEM clone (Incyte Genomics) containing the BLBP cDNA insert spotted on the microarray. (C) Quantitative real-time PCR of BLBP normalized to GAPDH resulted in a 145-fold change over expression in Nf1−/− TXF cells compared to wild-type mouse Schwann cells. Rn, fluorescent signal intensity; horizontal starred line, chosen threshold at geometric phase of amplification.

Article Snippet: In DRGN cocultures, neurofilament was visualized by incubation with anti-NF-15g1 antibodies ( 38 ) diluted 1:5, followed by donkey anti-mouse Cy3-labeled secondary antibodies (Jackson Immunoresearch).

Techniques: Expressing, Mutagenesis, Microarray, Genome Wide, Labeling, Generated, Sequencing, Software, Reverse Transcription Polymerase Chain Reaction, Amplification, Plasmid Preparation, Positive Control, Real-time Polymerase Chain Reaction, Over Expression

Journal:

Article Title: Brain Lipid Binding Protein in Axon-Schwann Cell Interactions and Peripheral Nerve Tumorigenesis

doi: 10.1128/MCB.23.6.2213-2224.2003

Figure Lengend Snippet: Mouse neuron-Schwann cell coculture. Anti-BLBP promotes extension of Nf1−/− TXF cell processes along axons. Wild-type (A and B) or Nf1−/− TXF (C and D) mouse Schwann cells labeled with Cell Tracker green were preincubated with rabbit IgG (A and C) or anti-BLBP antibodies (B and D) and seeded onto DRGN cultures stripped of endogenous Schwann cells. Two days after seeding, cocultures were fixed and stained with antineurofilament antibodies followed by Cy3 (red)-conjugated secondary antibodies. Confocal images obtained with Zeiss LSM Image Browser software are shown. Single cells are representative of the majority observed with each treatment. Arrowheads indicate Schwann cell processes. The asterisk indicates the region which is magnified fivefold in the inset. The scale bar in panel C equals 5 μm and also applies to panels A, B, and D. (E) Lower magnification (scale bar, 5 μm) of Nf1−/− TXF on DRGN cultures in the presence of anti-BLBP antibodies. Arrowheads indicate processes from two cells extending along neurites; other cells lack processes. (F) Extension of Nf1−/− TXF cell processes in the presence of anti-BLBP antibodies is statistically significant. The percentages of Nf1−/− TXF cells extending processes along axons in the presence of control IgG (gray bar) or anti-BLBP antibodies (black bar) are graphed. Error bars reflect standard deviations in a Student t test (P = 0.003).

Article Snippet: In DRGN cocultures, neurofilament was visualized by incubation with anti-NF-15g1 antibodies ( 38 ) diluted 1:5, followed by donkey anti-mouse Cy3-labeled secondary antibodies (Jackson Immunoresearch).

Techniques: Labeling, Staining, Software

Journal: Immunity

Article Title: Expression of the DNA-Binding Factor TOX Promotes the Encephalitogenic Potential of Microbe-Induced Autoreactive CD8 + T Cells

doi: 10.1016/j.immuni.2018.04.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Goat-anti-mouse Fab fragment , Jackson Immunoresearch , Cat# 115-006-006.

Techniques: Virus, Recombinant, Cell Isolation, Staining, Cytotoxicity Assay, Sample Prep, Luciferase, cDNA Synthesis, SYBR Green Assay, Infection, Microarray, Generated, shRNA, Sequencing, Software, Cytometry

Journal: eLife

Article Title: FABP4-mediated lipid accumulation and lipolysis in tumor-associated macrophages promote breast cancer metastasis

doi: 10.7554/eLife.101221

Figure Lengend Snippet:

Article Snippet: Antibody , Alexa Fluor 594-conjugated AffiniPure mouse anti-goat IgG polyclonal , Jackson ImmunoResearch , Cat#205-605-108 , 1:2000.

Techniques: Concentration Assay, Staining, Saline, SYBR Green Assay, Red Blood Cell Lysis, Cell Culture, XF Assay, Reverse Transcription, Polymer, Plasmid Preparation, Blocking Assay, Enzyme-linked Immunosorbent Assay, Sequencing, Transfection, Recombinant, Microarray, Gene Expression, Expressing, Derivative Assay, Real-time Polymerase Chain Reaction, Software, Sterility, Migration, Pore Size, Flow Cytometry, Quantitative RT-PCR, Imaging, Microscopy, Transmission Assay, Electron Microscopy

Journal: bioRxiv

Article Title: GNL3 regulates replication origin firing and protects stalled replication forks

doi: 10.1101/2022.10.27.514025

Figure Lengend Snippet: A . Flow cytometry experiment of HeLa S3 cells. Nascent DNA was labelled with IdU and total DNA stained with propidium iodide. B . Quantification of the intensity of IdU signal from flow cytometry analysis. For statistical analysis Mann-Whitney test was used; ****p<0.0001. C . Western-blot analysis of the indicated proteins upon chromatin fractionation. D . Quantification of chromatin fractionation based on 3 independent experiments. E . DNA combing experiment. HeLa S3 cells were subjected to two consecutive 20 min pulses of IdU and CldU and analyzed by DNA combing. A representative microscopy image of combed DNA molecules containing IdU (red) and CldU (green) tracks in presented with arrows indicating the direction of replication. F . Analysis of replication forks velocity by DNA combing. For statistical analysis Mann-Whitney test was used; ****p<0.0001. G . Analysis of GIFD (Global Instant Fork Density) by DNA combing in HeLa S3 cells. For statistical analysis paired t-test was used; *p<0.05. H . Replication timing experiment. HeLa S3 cells were pulse-labelled with BrdU for 90 min and sorted by flow cytometry in two fractions, S1 and S2, corresponding to early and late S-phase. Neo-synthesized DNA was immunoprecipitated with BrdU antibodies. Early and late neo-synthesized DNAs were labeled with Cy3 and Cy5 and hybridized on microarrays. After analyzing with the START-R software, replication-timing profiles can be obtained from two replicates. Shown are the zoomed microarray profiles of the timing of replication on chromosome 1 and chromosome 15 as example. Blue lines represent replication timing from siControl cells and red lines represent siGNL3 cells and grey spots represent the log ratio intensity for each probes of the microarray. Any significantly disturbed regions are detected by START-R software.

Article Snippet: The following secondary antibodies were used: Alexa fluor 488 anti-mouse antibody (Life A21241) and Cy3 anti-rat antibody (Jackson Immunoresearch 712-166-153).

Techniques: Flow Cytometry, Staining, MANN-WHITNEY, Western Blot, Fractionation, Microscopy, Synthesized, Immunoprecipitation, Labeling, Software, Microarray

Journal:

Article Title: Deletion of the COOH-Terminal Domain of CXC Chemokine Receptor 4 Leads to the Down-regulation of Cell-to-Cell Contact, Enhanced Motility and Proliferation in Breast Carcinoma Cells

doi: 10.1158/0008-5472.CAN-05-3579

Figure Lengend Snippet: Subcellular distribution and trafficking of CXCR4-WT and CXCR4-DCTD. A, CXCR4-ΔCTD exhibited increased intracellular localization. MCF-7/Vector, MCF-7/CXCR4-WT, and MCF-7/CXCR4-ΔCTD cells were grown on glass coverslips in complete growth medium, fixed, permeabilized, and stained with an αCXCR4 antibody (clone 12G5, MAB170) followed by an Alexa 594–conjugated α-mouse IgG. Fluorescent images were captured with 0.1 μm Z-stack using a Zeiss Axiophot upright microscope. The expression of CXCR4 on cell surface was analyzed by FACS analysis using antibodies as indicated. B, truncated CXCR4 interacts and colocalizes with endogenous β-arrestin (β-arr). Cells were serum starved overnight and stimulated with/without 500 ng/mL CXCL12 for 5 minutes at 37°C. The cells were fixed with 4% paraformaldehyde and permeabilized with 0.2% Triton X-100. CXCR4 was probed with mouse monoclonal antibody (clone 12G5, MAB170) and β-arrestin2 with goat polyclonal anti-β-arrestin2 antibody (cross-reacts to a lesser extent to β-arrestin1, sc-6387). The receptor was visualized with Cy3 donkey anti-mouse antibody (715-165-150, Jackson ImmunoResearch) and β-arrestin2 was visualized through sequential binding of rabbit anti-goat antibody (BA-5000, Vector Laboratories, Burlingame, CA) and Cy5-donkey anti-rabbit antibody (711-175-152, Jackson ImmunoResearch). White arrows, vesicles where CXCR4 receptor and β-arrestin2 colocalize in transduced MCF-7 cells.

Article Snippet: The receptor was visualized with Cy3 donkey anti-mouse antibody (715-165-150, Jackson ImmunoResearch) and β-arrestin2 was visualized through sequential binding of rabbit anti-goat antibody (BA-5000, Vector Laboratories, Burlingame, CA) and Cy5-donkey anti-rabbit antibody (711-175-152, Jackson ImmunoResearch).

Techniques: Plasmid Preparation, Staining, Microscopy, Expressing, Binding Assay

Journal:

Article Title: Deletion of the COOH-Terminal Domain of CXC Chemokine Receptor 4 Leads to the Down-regulation of Cell-to-Cell Contact, Enhanced Motility and Proliferation in Breast Carcinoma Cells

doi: 10.1158/0008-5472.CAN-05-3579

Figure Lengend Snippet: Differential gene expression revealed that mesenchymal-related genes are up-regulated and epithelial-related genes are down-regulated in MCF-7/CXCR4-ΔCTD cells. A, RNA integrity index. Total RNA was isolated from MCF-7/Vector, MCF-7/CXCR4-WT, and MCF-7/ΔCTD cells and treated with DNase. The electrophoresis of RNA in the Eukaryote Total RNA Nano-DE114000902 resulted in a 99 percentile RNA integrity index value. B, list of differentially expressed genes identified by microarray analysis. MCF-7/CXCR4-WT-derived total RNA was reverse transcribed into cDNA with Cy5 labeling. MCF-7/Vector-derived RNA and MCF-7/CXCR4-ΔCDT-derived RNA were reverse transcribed into cDNA with Cy3 labeling. The labeled cDNA was hybridized to a human 30,000 oligoarray and the fluorescent ratio, Cy5/Cy3, was analyzed with GeneSpring software. The array data in Supplementary Data are represented as the fold change in gene expression comparing the gene expression in MCF-7/CXCR4-WT cells with that in MCF-7/Vector cells and comparing the gene expression in MCF-7/CXCR4-WT cells with that in MCF-7/CXCR4-ΔCTD cells. The genes possibly related to cell proliferation and EMT in this array analysis are listed in the table and the relationship between these genes is graphed (Fig. 5B). WT, MCF-7/CXCR4-WT cells; ΔCTD, MCF-7/CXCR4-ΔCTD cells; Vector, MCF-7/Vector cells; ↔, not a significant differential expression ratio (<3-fold) of Cy5/Cy3. In Supplementary Data I and II, all up-regulated or down-regulated genes with >3-fold differences in expression are listed.

Article Snippet: The receptor was visualized with Cy3 donkey anti-mouse antibody (715-165-150, Jackson ImmunoResearch) and β-arrestin2 was visualized through sequential binding of rabbit anti-goat antibody (BA-5000, Vector Laboratories, Burlingame, CA) and Cy5-donkey anti-rabbit antibody (711-175-152, Jackson ImmunoResearch).

Techniques: Gene Expression, Isolation, Plasmid Preparation, Electrophoresis, Microarray, Derivative Assay, Reverse Transcription, Labeling, Software, Quantitative Proteomics, Expressing

Journal: Cancer Cell

Article Title: MST4 Phosphorylation of ATG4B Regulates Autophagic Activity, Tumorigenicity, and Radioresistance in Glioblastoma

doi: 10.1016/j.ccell.2017.11.005

Figure Lengend Snippet:

Article Snippet: Peroxidase-IgG Fraction Monoclonal Mouse Anti-Rabbit IgG, Light Chain Specific , Jackson ImmunoResearch Laboratories , Cat# 211-032-171; RRID: AB_2339149.

Techniques: Plasmid Preparation, Recombinant, Staining, Protease Inhibitor, Lysis, Mutagenesis, Gel Extraction, Microarray, DNA Methylation Assay, DNA Sequencing, shRNA, Control, Software

Journal: Cell reports

Article Title: Neuraminidase 1 regulates neuropathogenesis by governing the cellular state of microglia via modulation of Trem2 sialylation

doi: 10.1016/j.celrep.2024.115204

Figure Lengend Snippet:

Article Snippet: Peroxidase AffiniPure TM goat anti-rabbit IgG (H + L) , Jackson ImmunoResearch Laboratory , 111-035-003 RRID:AB_2313567.

Techniques: Virus, Recombinant, Labeling, Plasmid Preparation, Magnetic Beads, Enzyme-linked Immunosorbent Assay, Isolation, Microarray, Staining, Software, Lysis

Journal: Cancer cell

Article Title: SETD5-Coordinated Chromatin Reprogramming Regulates Adaptive Resistance to Targeted Pancreatic Cancer Therapy

doi: 10.1016/j.ccell.2020.04.014

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Peroxidase-conjugated Mouse Anti-Rabbit IgG, light chain specific , Jackson ImmunoResearch , Cat# 211-032-171; RRID: AB_2339149.

Techniques: Virus, Recombinant, Protease Inhibitor, Sequencing, Modification, Membrane, Plasmid Preparation, Purification, Bicinchoninic Acid Protein Assay, Staining, Silver Staining, Mutagenesis, Glutathione Assay, Transfection, Control, Software, Microarray

Journal:

Article Title: Use of Oligonucleotide Microarrays for Rapid Detection and Serotyping of Acute Respiratory Disease-Associated Adenoviruses

doi: 10.1128/JCM.42.7.3232-3239.2004

Figure Lengend Snippet: Microarray-based detection of Ad3 contamination of an ATCC Ad4 stock (VR-4) and cell culture verification. (A) Multiplex PCR and microarray analysis suggested the presence of two adenoviral serotypes (Ad3 and Ad4) in ATCC VR-4. A-549 cells were inoculated with ATCC VR-4 and immunostained at 72 h postinfection with Ad4-specific rabbit antiserum (B), Ad3-specific rabbit antiserum (C), or Ad7a-specific rabbit antiserum (D) and a fluorescein isothiocyanate-conjugated secondary anti-rabbit antibody. The white arrowheads in panels B and C indicate characteristic adenoviral nuclear inclusions (not seen in panel D), confirming the presence of both Ad3 and Ad4 in ATCC VR-4.

Article Snippet: All infected samples were processed in parallel and were stained with either Ad3 rabbit antiserum (VR-1080AS/RB), Ad4 rabbit antiserum (VR-1081AS/RB), or Ad7a rabbit antiserum (VR-1084AS/RB) (ATCC) and visualized with a fluorescein isothiocyanate (FITC)-conjugated goat anti-rabbit IgG secondary antibody (Jackson ImmunoResearch, West Grove, Pa.).

Techniques: Microarray, Cell Culture, Multiplex Assay