Journal: Scientific Data

Article Title: Genome-wide expression datasets of anti-VEGF and dexamethasone treatment of angiogenesis in the rat cornea

doi: 10.1038/sdata.2017.111

Figure Lengend Snippet: (1) sutures were placed intrastromally into the temporal cornea, and immediately followed by topical application of eye drops (IgG, anti- Vegf or dexamethasone). Eye drops were applied until the 48 h time point. At t=48 h, IVCM and slit lamp data was collected and used for phenotypic characterisation. (2) cornea tissue was harvested and used for RNA extraction, and RNA quality verified. (3) high quality RNA was used for target preparation for microarray hybridisation on to GeneChip Rat 230 2.0 microarray chips. The microarray chips were scanned and image files acquired. (4) CEL files were normalised using expression console software. The generated CHP together with the CEL files were submitted to Gene Expression Omnibus repository.

Article Snippet: Three groups of six rats each were treated with one of three topical treatments: IgG (Cat. No. 108-C, R&D Systems) at 20 μgml −1 , anti- Vegf (Cat. No AF 564, a neutralizing rat-specific goat polyclonal pan-VEGFA antibody, R&D Systems, Minneaplois MN, USA) at 20 μgml −1 or dexamethasone (Opnol, Clean Chemical, Sweden AB, Borlänge, Sweden) at 1 mgml −1 .

Techniques: Eye Drops, RNA Extraction, Microarray, Hybridization, Expressing, Software, Generated, Gene Expression

Journal: Scientific Data

Article Title: Genome-wide expression datasets of anti-VEGF and dexamethasone treatment of angiogenesis in the rat cornea

doi: 10.1038/sdata.2017.111

Figure Lengend Snippet: Dataset and sample description across treatment groups.

Article Snippet: Three groups of six rats each were treated with one of three topical treatments: IgG (Cat. No. 108-C, R&D Systems) at 20 μgml −1 , anti- Vegf (Cat. No AF 564, a neutralizing rat-specific goat polyclonal pan-VEGFA antibody, R&D Systems, Minneaplois MN, USA) at 20 μgml −1 or dexamethasone (Opnol, Clean Chemical, Sweden AB, Borlänge, Sweden) at 1 mgml −1 .

Techniques: Microarray, Control

Journal: Scientific Data

Article Title: Genome-wide expression datasets of anti-VEGF and dexamethasone treatment of angiogenesis in the rat cornea

doi: 10.1038/sdata.2017.111

Figure Lengend Snippet: ( a – d ) are signal intensity values correlated between control, IgG, anti- Vegf and dexamethasone treated samples respectively. ( e ) is an example of pathway enrichment analysis and ( f ) is a display of the genes involved in a selected pathway (PI3K-Akt signalling pathway).

Article Snippet: Three groups of six rats each were treated with one of three topical treatments: IgG (Cat. No. 108-C, R&D Systems) at 20 μgml −1 , anti- Vegf (Cat. No AF 564, a neutralizing rat-specific goat polyclonal pan-VEGFA antibody, R&D Systems, Minneaplois MN, USA) at 20 μgml −1 or dexamethasone (Opnol, Clean Chemical, Sweden AB, Borlänge, Sweden) at 1 mgml −1 .

Techniques: Control

Journal: American Journal of Physiology - Lung Cellular and Molecular Physiology

Article Title: VEGF in the lung: a role for novel isoforms

doi: 10.1152/ajplung.00353.2009

Figure Lengend Snippet: Representative expression of VEGF xxx b expression in normal and acute respiratory distress syndrome (ARDS) lung detected by immunocytochemistry. A and C are IgG isotopic controls, normal and ARDS lung, respectively. In B , extensive VEGF xxx b is present in normal lung, particularly in alveolar type II (ATII) cells (arrow). In D , there is much less VEGF xxx b staining in the lung tissue per se, but more is present in infiltrating inflammatory cells (arrow).

Article Snippet: After three washes with PBST, 100 μl/well of a biotinylated goat polyclonal antibody anti-human Pan VEGF (AF293B, R&D Systems), at 50 ng/ml in PBS, was added.

Techniques: Expressing, Immunocytochemistry, Staining

Journal: American Journal of Physiology - Lung Cellular and Molecular Physiology

Article Title: VEGF in the lung: a role for novel isoforms

doi: 10.1152/ajplung.00353.2009

Figure Lengend Snippet: ELISA performed on bronchoalveolar lavage fluid from healthy control subjects, patients “at risk,” and with ARDS ( n = 8) showing a significant reduction in VEGF 165 b in at-risk subjects compared with healthy controls (* P < 0.05).

Article Snippet: After three washes with PBST, 100 μl/well of a biotinylated goat polyclonal antibody anti-human Pan VEGF (AF293B, R&D Systems), at 50 ng/ml in PBS, was added.

Techniques: Enzyme-linked Immunosorbent Assay, Control

Journal: Scientific Reports

Article Title: Genome-wide expression differences in anti- Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea

doi: 10.1038/s41598-017-07129-4

Figure Lengend Snippet: Limbal vessel dilation, inflammatory cell infiltration and Vegfa expression following IgG, anti- Vegf and dexamethasone treatment of suture-induced injury in the rat cornea. ( A ) Slit lamp photographs depicting limbal vessel dilation and looping angiogenesis 48 h after suture placement in IgG and anti- Vegf groups, not detected in the dexamethasone group; expanded view of the white boxed area in ( B ). ( C ) IVCM images of limbal vessel dilation, and the corresponding measurements of limbal vessel diameter in ( G ); ( D ) Microscopic images of aqueous humor cellular content, and the corresponding quantification in ( H ). ( E ) Immunofluorescence of Vegfa (green) and DAPI counterstaining of nuclei (blue) in corneal tissue sections. ( F ) CD31 staining (green) of naïve and sutured cornea at 48 hours: the latter shows no sign of corneal neovascularization. n = 4 corneas per group for ( G) and ( H) , *P < 0.05; **P < 0.01; ***P < 0.001; n.s. = P > 0.05 and error bars represent SD.

Article Snippet: The time of suture placement was designated as 0 h. Sutured animals were randomly assigned to one of three topical treatment groups: Rat-specific goat polyclonal pan- Vegf antibody (20 μg/ml, Cat. No AF 564, R&D Systems, Minneapolis MN, USA).

Techniques: Expressing, Immunofluorescence, Staining

Journal: Scientific Reports

Article Title: Genome-wide expression differences in anti- Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea

doi: 10.1038/s41598-017-07129-4

Figure Lengend Snippet: Differentially expressed genes (DEGs) in IgG, dexamethasone and anti- Vegf treated groups, and selected enriched biological processes. ( A–C) Volcano plots of the DEGs in IgG, dexamethasone and anti- Vegf groups respectively. (D) Selected biological processes of interest, indicating the number of DEGs involved in the processes for each treatment.

Article Snippet: The time of suture placement was designated as 0 h. Sutured animals were randomly assigned to one of three topical treatment groups: Rat-specific goat polyclonal pan- Vegf antibody (20 μg/ml, Cat. No AF 564, R&D Systems, Minneapolis MN, USA).

Techniques:

Journal: Scientific Reports

Article Title: Genome-wide expression differences in anti- Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea

doi: 10.1038/s41598-017-07129-4

Figure Lengend Snippet: The top 10 differentially up- and downregulated genes involved in selected biological processes (a), and in selected pathways (b).

Article Snippet: The time of suture placement was designated as 0 h. Sutured animals were randomly assigned to one of three topical treatment groups: Rat-specific goat polyclonal pan- Vegf antibody (20 μg/ml, Cat. No AF 564, R&D Systems, Minneapolis MN, USA).

Techniques:

Journal: Scientific Reports

Article Title: Genome-wide expression differences in anti- Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea

doi: 10.1038/s41598-017-07129-4

Figure Lengend Snippet: Pathway enrichment analysis indicates that dexamethasone suppresses most DEGs in all selected inflammatory and angiogenesis pathways, relative to IgG and anti- Vegf treatment.

Article Snippet: The time of suture placement was designated as 0 h. Sutured animals were randomly assigned to one of three topical treatment groups: Rat-specific goat polyclonal pan- Vegf antibody (20 μg/ml, Cat. No AF 564, R&D Systems, Minneapolis MN, USA).

Techniques:

Journal: Scientific Reports

Article Title: Genome-wide expression differences in anti- Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea

doi: 10.1038/s41598-017-07129-4

Figure Lengend Snippet: ( A–G ): Immunofluorescent staining of naïve, and sutured corneas from treatment groups (48 h post-suture). Factors most differentially regulated between dexamethasone and anti- Vegf groups from microarray analysis are shown. Expression signals are indicated in green, and DAPI counterstained nuclei in blue. Scale bar = 50 µm. ( H–J ): qPCR analysis of C3 , C1s and Vegfa gene expression. The error bars represent SEM.

Article Snippet: The time of suture placement was designated as 0 h. Sutured animals were randomly assigned to one of three topical treatment groups: Rat-specific goat polyclonal pan- Vegf antibody (20 μg/ml, Cat. No AF 564, R&D Systems, Minneapolis MN, USA).

Techniques: Staining, Microarray, Expressing, Gene Expression

Journal: Scientific Reports

Article Title: Genome-wide expression differences in anti- Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea

doi: 10.1038/s41598-017-07129-4

Figure Lengend Snippet: Summary of genes involved in the complement cascade from gene microarray analysis, and the FC Diff and the corresponding P values.

Article Snippet: The time of suture placement was designated as 0 h. Sutured animals were randomly assigned to one of three topical treatment groups: Rat-specific goat polyclonal pan- Vegf antibody (20 μg/ml, Cat. No AF 564, R&D Systems, Minneapolis MN, USA).

Techniques: Microarray, Binding Assay, Virus

Journal: Scientific Reports

Article Title: Genome-wide expression differences in anti- Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea

doi: 10.1038/s41598-017-07129-4

Figure Lengend Snippet: Summary of complement genes differentially regulated by dexamethasone treatment relative to anti- Vegf , and their roles in the complement cascade based on gene expression microarray analysis. Differentially regulated genes (upregulated genes labelled in red, downregulated genes in green) are shown along with their fold change difference (dexamethasone minus anti- Vegf ) and corresponding p-value (between dexamethasone and anti- Vegf fold change) given in parentheses. All differentially regulated genes mapped to the classical pathway, while Cfi , a natural inhibitor of C3 and C5 convertase production, was strongly downregulated. This, combined with strong upregulation of C3 , promoted pathways leading to inflammatory cell activation and invasion into the cornea following dexamethasone treatment. Further downstream complement components ( C6 – C9 ) leading to cell lysis were not differentially regulated by dexamethasone. The figure is an adapted version of the conceptual diagram presented by del Zoppo .

Article Snippet: The time of suture placement was designated as 0 h. Sutured animals were randomly assigned to one of three topical treatment groups: Rat-specific goat polyclonal pan- Vegf antibody (20 μg/ml, Cat. No AF 564, R&D Systems, Minneapolis MN, USA).

Techniques: Gene Expression, Microarray, Activation Assay, Lysis

Journal: Cancer Research

Article Title: VEGF165b, an Inhibitory Vascular Endothelial Growth Factor Splice Variant

doi: 10.1158/0008-5472.can-04-0934

Figure Lengend Snippet: Fig. 2. A, western blot of recombinant VEGF165b and VEGF165 probed with antibodies to VEGF165b and all iso- forms. The VEGF165b antibody specifically detects the VEGF165b isoform, whereas the pan-VEGF antibody detects both isoforms. B, ELISA for VEGF165b and VEGF165. In- creasing concentrations of recombinant human VEGF165b or VEGF165b were assayed with the ELISA described in Mate- rials and Methods, with either VEGF165b antibody (f) or pan-VEGF antibody (). Both ELISAs detected respective VEGF isoforms at concentrations 100 pgml-1.

Article Snippet: Membranes were stripped with enhanced chemiluminescence stripping buffer and probed with a pan VEGF primary antibody [VEGF-(C-1); Santa Cruz Biotechnology] 1:100 dilution in 5% Marvel–PBS-T for recombinant proteins, and 1:200 dilution for transurethral resection of the prostate chip proteins) overnight at 4°C.

Techniques: Western Blot, Recombinant, Enzyme-linked Immunosorbent Assay

Journal: Cancer Research

Article Title: VEGF165b, an Inhibitory Vascular Endothelial Growth Factor Splice Variant

doi: 10.1158/0008-5472.can-04-0934

Figure Lengend Snippet: Fig. 4. VEGFxxxb proteins are found in normal human cells, tissue, and plasma. A, terminally differentiated human podocyte protein extracts were probed with anti-VEGF antibody. This revealed multiple bands corresponding to multiple splice variants of VEGF. When this blot was stripped and reprobed with the anti-VEGF165b antibody, bands appeared consistent with sister splice variants of the common isoforms. VEGF isoforms can be either dimers or monomers, and these bands are consistent with a monomer of VEGF121b (14 kDa, band a), and dimers of VEGF121b (28 kDa, band b), VEGF145b (33 kDa, band c), VEGF165b (38 kDa, band d), and VEGF189b (43.5 kDa, band e) were detected. A series of bands 84 kDa (bands at f) are consistent with large VEGFxxxb isoforms. B, transurethral resection of the prostate tissue probed with VEGFxxxb and pan VEGF antibody also shows expression of multiple isoforms. C, immunohistochemistry of human glomeruli with anti-VEGF165b antibody (i, ii) or nonspecific mouse IgG (iii, iv). This showed that VEGFxxxb was expressed in podocytes on the periphery of the glomerular tuft (arrows). Scale bar is 20 m. D, an ELISA with the VEGF165b antibody was used to detect VEGFxxxb protein in human plasma and tissues. Significant protein expression was seen in normal plasma and benign prostate tissue. A lower level of protein expression was detected in malignant prostate samples. E. mRNA for VEGF165b was expressed in benign (14 of 17) but not malignant (2/9) prostate tissues, whereas VEGF165 isoforms were equally present in both tissue types. Lanes 1, 2, and 3 are benign samples, W is water, b is recombinant VEGF165b cDNA, and a is recombinant VEGF165 cDNA. 7827

Article Snippet: Membranes were stripped with enhanced chemiluminescence stripping buffer and probed with a pan VEGF primary antibody [VEGF-(C-1); Santa Cruz Biotechnology] 1:100 dilution in 5% Marvel–PBS-T for recombinant proteins, and 1:200 dilution for transurethral resection of the prostate chip proteins) overnight at 4°C.

Techniques: Clinical Proteomics, Expressing, Immunohistochemistry, Enzyme-linked Immunosorbent Assay, Recombinant