plasmid dna (Amaxa)
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Plasmid Dna, supplied by Amaxa, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 86 stars, based on 1 article reviews
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1) Product Images from "Negative regulation of the SH2-homology–containing protein-tyrosine phosphatase-1 (SHP-1) P2 promoter by the HTLV-1 Tax oncoprotein"
Article Title: Negative regulation of the SH2-homology–containing protein-tyrosine phosphatase-1 (SHP-1) P2 promoter by the HTLV-1 Tax oncoprotein
Journal: Blood
doi: 10.1182/blood-2006-11-058388

Figure Legend Snippet: Repression of wt P2 promoter activity by Tax. (A) Fresh CD4 + cells were transfected with HTLV-1 provirus pACH-wtTax DNA using Amaxa Kit. Cells were then cultured in AIM-V media with 10% fetal bovine serum, IL-2 (100 U/mL), and PHA (1 μg/mL). Cell
Techniques Used: Activity Assay, Transfection, Cell Culture
2) Product Images from "Defective autophagy in vascular smooth muscle cells accelerates senescence and promotes neointima formation and atherogenesis"
Article Title: Defective autophagy in vascular smooth muscle cells accelerates senescence and promotes neointima formation and atherogenesis
Journal: Autophagy
doi: 10.1080/15548627.2015.1096485

Figure Legend Snippet: SQSTM1 accumulation links defective VSMC autophagy to senescence. ( A ) Atg7 +/+ VSMCs were transfected with 5 µg plasmid DNA encoding SQSTM1 (SQSTM1+). Four d after transfection, VSMCs were analyzed for SQSTM1, CDKN2A, phospho RB and total RB expression by western blotting. ( B , C ) SQSTM1 overexpressing VSMCs were incubated with BrdU ( B ) to examine proliferation capacity (***, P
Techniques Used: Transfection, Plasmid Preparation, Expressing, Western Blot, Incubation
3) Product Images from "Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage"
Article Title: Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage
Journal: Nature Communications
doi: 10.1038/s41467-019-13894-9

Figure Legend Snippet: DNA damage promotes the generation and secretion of extracellular vesicles (EVs) in Er1 F/− macrophages. a Schematic representation of the high-throughput MS analysis in Er1 F/− compared to Er1 F/+ BMDMs media. b Venn’s diagram of proteins identified in Er1 F/− media from two independent biological replicates. c List of significantly over-represented GO terms associated with Cellular Component. d Number of observed (obs.) and expected (exp.) known protein interactions within the core 211 shared proteins set. e Schematic representation of the major protein complex identified in BMDM media. f Western blot analysis of CD9, ALIX, RAB10, and RAC1 proteins levels in the EV fraction of Er1 F/− and Er1 F/+ sera ( n = 6; see also Supplementary Fig. 5A ; left panel). g Transmission electron microscopy of EVs marking the presence of exosomes with a size 30–80 nm in Er1 F/− TEM media. h Western blot analysis of CD9, ALIX, RAB10, RAC2, and RAC1 proteins levels in Er1 F/− compared to Er1 F/+ EV fraction of BMDM media ( n = 5). A graph showing the fold change and statistical significance of the indicated protein levels is shown in Supplementary Fig. 5A ; right panel. i Western blot analysis of CD9, ALIX, RAB10, RAC2, and RAC1 proteins levels in the EV fraction of media derived from the MMC-treated and control BMDMs exposed to ATM (ATMi) or ATR (ATRi) inhibitors (as indicated; n = 3). A graph showing the fold change and statistical significance of the indicated protein levels is shown in Supplementary Fig. 5C . j IL8 and IL6 protein levels in Er1 F/− and Er1 F/+ sera and BMDM media (as indicated). k Immunofluorescence detection of RAC1 (~500 cells per genotype), RAB10 (~150 cells per genotype) and RAC2 (~150 cells per genotype) in Er1 F/− and Er1 F/+ PPCs ( n > 400 cells per genotype) (see also Supplementary Fig. 5e for RHOA), l hepatocytes ( n > 100 cells per genotype) and m thioglycolate-elicited macrophages (TEMs) ( n > 500 cells per genotype). Colored numbers indicate the average percentage of positively stained cells ± SEM for the indicated, color-matched protein. Error bars indicate S.E.M. among replicates ( n ≥ 3). Asterisk indicates the significance set at p -value: *≤0.05, **≤0.01 (two-tailed Student’s t -test). (nd): not detected. Gray line is set at 5 μm scale.
Techniques Used: High Throughput Screening Assay, Mass Spectrometry, Western Blot, Transmission Assay, Electron Microscopy, Transmission Electron Microscopy, Derivative Assay, Immunofluorescence, Staining, Two Tailed Test

Figure Legend Snippet: DNA damage accumulation in Er1 F/− macrophages. a Lys- Cre -driven Rosa-YFP expression in thioglycolate-elicited peritoneal macrophages (TEMs; n > 500 cells counted per genotype). The numbers indicate the average percentage of GFP (+) cells ± SEM), b Lys- Cre -driven Rosa-YFP expression in hepatocytes and primary pancreatic cells (PPCs) shown by confocal microscopy ( n > 100 cells counted per genotype; the numbers indicate the average percentage of GFP (+) cells ± SEM) and c western blotting. d Immunofluorescence staining of Lys- Cre -driven Rosa-YFP expression in the Er1 F/− pancreas and the white adipose tissue (WAT) that are infiltrated with MAC1-positive macrophages (indicated by the arrowheads). e Western blotting of ERCC1 protein in whole-cell (w) cytoplasmic (c) and nuclear (n) extracts. Tubulin (TUB), and Fibrillarin (FIB) were used as loading controls (as indicated). The graph represents the fold change (F.C.) of ERCC1 protein levels in Er1 F/− samples compared to corresponding Er1 F/+ controls ( n = 3). f Cell type-specific ablation of ERCC1 (indicated by the arrowhead) in bone marrow-derived (BMDMs) and TEMs expressing the macrophage-specific antigen MAC1. The numbers indicate the average percentage of ERCC1 (+) nuclei ± SEM in Er1 F/+ and Er1 F/− BMDMs and TEMs ( n > 150 cells were counted per genotype). g Immunofluorescence detection of γ-H2AX in Er1 F/− and Er1 F/+ BMDMs and h TEMs. i Immunofluorescence detection of FANCI, pATM and RAD51 in Er1 F/− and Er1 F/+ BMDMs (in each case n > 200 cells were counted per genotype). j Immunofluorescence detection of pATM in Er1 F/− and Er1 F+ TEMs ( n > 150 cells were counted per genotype). k Immunofluorescence detection of Caspase 3 (CASP3) ( n > 300 cells were counted per genotype) and l GL13 (indicated by the arrowhead), commercially available SenTraGor®, in Er1 F/− and Er1 F+ BMDMs. Fluorescence intensity was calculated in n > 50 cells per genotype. Gray line is set at 5 μm scale, unless otherwise indicated. Error bars indicate S.E.M. among replicates ( n ≥ 3). Asterisk indicates the significance set at p -value: *≤0.05, **≤0.01 (two-tailed Student’s t -test).
Techniques Used: Expressing, Confocal Microscopy, Western Blot, Immunofluorescence, Staining, Derivative Assay, Fluorescence, Two Tailed Test
4) Product Images from "Easy quantitative assessment of genome editing by sequence trace decomposition"
Article Title: Easy quantitative assessment of genome editing by sequence trace decomposition
Journal: Nucleic Acids Research
doi: 10.1093/nar/gku936

Figure Legend Snippet: Application of TIDE to in vivo edited DNA sequences. ( a–d ) A pool of human K562 cells expressing GFP treated with Cas9 alone (control) and cells treated with Cas9 and a GFP targeting sgRNA (sample) were analyzed by: TIDE (a and b), sequence analysis of 84 cloned DNA fragments (c) and flow cytometry (d). ( a ) Indel spectrum determined by TIDE. Inset shows the estimated composition of the inserted base for the +1 insertion. ( b ) Aberrant nucleotide signal of the sample (green) compared to that of the control (black). Blue dotted line indicates the expected cutting site. Gray horizontal bar shows the region used for decomposition. ( c ) Comparison of indel occurrences in cloned DNA fragments ( n = 84) to frequencies estimated by TIDE, with P -values according to Pearson's chi-squared test. Decomposition was limited to indels of size 0-10, hence larger indels could not be detected. ( d ) Distributions of GFP fluorescence intensities of Cas9 and Cas9+sgRNA treated cells, measured by flow cytometry. The percentage of GFP-positive cells is indicated in the top right corner within indicated histogram gate. ( e–h ) TIDE analysis of various endogenous genes (NDC1, LBR, LMN) targeted with RGENs in human cell lines (K562, RPE) and in a Drosophila cell line (Kc167). Insets: prediction of the inserted base for +1 insertions.
Techniques Used: In Vivo, Expressing, Sequencing, Clone Assay, Flow Cytometry, Cytometry, Fluorescence
5) Product Images from "ZEB1 turns into a transcriptional activator by interacting with YAP1 in aggressive cancer types"
Article Title: ZEB1 turns into a transcriptional activator by interacting with YAP1 in aggressive cancer types
Journal: Nature Communications
doi: 10.1038/ncomms10498

Figure Legend Snippet: ZEB1 functionally interacts with YAP. ( a , b ) Schematic representation of the promoter region of human CTGF ( a ) and CYR61 ( b ) genes on chromosomes 6q23.2 and 1p22.3, respectively. The potential ZEB1 (E-boxes) and YAP/ TEAD (MCAT) binding sites, the regions amplified after chromatin immunoprecipitation (ChIP) (blue arrows represent primer pairs) are depicted. Numbers indicate positions in bp on chromosomal DNA relative to the transcription start site (+1). Used luciferase ( luc2 ) reporter constructs with and without E-boxes analysed in MCF7 cells transiently transfected with ZEB1, YAP or empty vector control are shown; n =3. qPCR analysis after ChIPs for endogenously expressed ZEB1 and YAP in MDA-MB231 cells shows direct binding of both factors, the promoters of CTGF and CYR61 . HPRT1 is used as negative control; n =3. ( c ) qPCR analyses of anti-ZEB1/anti-YAP sequential ChIP (re-ChIP) of HEK293T cells overexpressing ZEB1 alone or in combination with V5-tagged YAP at the indicated gene loci (initial ChIP against ZEB1 and re-ChIP against V5). We confirmed that ZEB1 and YAP can simultaneously bind to the same region of the CTGF gene but not at the CDH1 and MIR200C loci, two genes repressed by ZEB1 and at control HPRT1 ; n =2. ( d ) CTGF-promoter reporter assay upon overexpression of ZEB1 and YAP expression constructs (YAP=wild type, del TA=without transactivation domain, del TB=without TEAD binding domain) in MCF7; n =3. ( e ) CTGF -promoter reporter constructs with sequential mutations in the three TEAD bindings sites (red crosses). Reporter assays in MCF7 cells showing that TEAD binding sites are important for functional interaction of ZEB1 and YAP; n =3. (f) Reporter constructs with four tandem repeats of wild-type or mutated (mut) TEAD binding sites upstream of a minimal promoter analysed in MCF7 cells showing that functional interaction of ZEB1 and YAP is transferred through TEAD binding sites n =3. For a – f , mean±s.e.m. For reporter assays, firefly luciferase activity was normalized to co-transfected renilla luciferase; * P =0.01–0.05, ** P =0.001–0.01, *** P =0.001–0.0001, **** P
Techniques Used: Binding Assay, Amplification, Chromatin Immunoprecipitation, Luciferase, Construct, Transfection, Plasmid Preparation, Real-time Polymerase Chain Reaction, Multiple Displacement Amplification, Negative Control, Reporter Assay, Over Expression, Expressing, Functional Assay, Activity Assay
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