mtdna content  (Qiagen)

 
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    Name:
    QIAamp DNA Mini Kit
    Description:
    For isolation of genomic mitochondrial bacterial parasite or viral DNA Kit contents Qiagen QIAamp DNA Mini Kit 50 preps 200L Sample 50 to 200L Elution Volume Whole Blood Tissue Cells Sample Silica Technology Spin Column Format Manual Processing 20 min Time Run 4 to 12g Yield Rapid Purification of High quality Ready to use DNA Ideal for PCR Southern Blotting For Isolation of Genomic Mitochondrial Bacterial Parasite or Viral DNA Includes 50 QIAamp Mini Spin Columns Proteinase K Reagents Buffers 2mL Collection Tubes Benefits Rapid purification of high quality ready to use DNA Consistent high yields Complete removal of contaminants and inhibitors
    Catalog Number:
    51304
    Price:
    165
    Category:
    QIAamp DNA Mini Kit
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    Structured Review

    Qiagen mtdna content
    QIAamp DNA Mini Kit
    For isolation of genomic mitochondrial bacterial parasite or viral DNA Kit contents Qiagen QIAamp DNA Mini Kit 50 preps 200L Sample 50 to 200L Elution Volume Whole Blood Tissue Cells Sample Silica Technology Spin Column Format Manual Processing 20 min Time Run 4 to 12g Yield Rapid Purification of High quality Ready to use DNA Ideal for PCR Southern Blotting For Isolation of Genomic Mitochondrial Bacterial Parasite or Viral DNA Includes 50 QIAamp Mini Spin Columns Proteinase K Reagents Buffers 2mL Collection Tubes Benefits Rapid purification of high quality ready to use DNA Consistent high yields Complete removal of contaminants and inhibitors
    https://www.bioz.com/result/mtdna content/product/Qiagen
    Average 90 stars, based on 15940 article reviews
    Price from $9.99 to $1999.99
    mtdna content - by Bioz Stars, 2020-07
    90/100 stars

    Images

    1) Product Images from "Resveratrol Ameliorates Mitophagy Disturbance and Improves Cardiac Pathophysiology of Dystrophin-deficient mdx Mice"

    Article Title: Resveratrol Ameliorates Mitophagy Disturbance and Improves Cardiac Pathophysiology of Dystrophin-deficient mdx Mice

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-33930-w

    Levels of mtDNA with deletion and tissue ROS were increased in the mdx mouse heart. ( A ) Schematic depicting the regions of the mouse mitochondrial genome (mtDNA) amplified by long-range PCR [nucleotide positions (np) 9984-3577 and np 3553–9990] and the qPCR methods. ( B ) mtDNA content determined by qPCR amplifying the D-loop and COX2 regions and nuclear RPS18 genome region. N = 4. ( C ) Representative gel images of long-range PCR of myocardial DNA samples. For quantification, the results of 10, 5, and 2.5 ng of DNA from an intact mouse heart per reaction were included. The nuclear Gapdh gene was amplified as an internal control. ( D ) Levels of long-range PCR products normalized to Gapdh . N = 4. ( E ) Representative Immunoblots for VDAC1, SDHA, Rieske, HSP60, and GAPDH. ( F ) Levels of mitochondrial proteins in the hearts. ( G ) Dihydroethidium (DHE) fluorescence (red) images in heart sections from 22-week-old control and mdx mice. ( H ) Relative DHE fluorescence intensity. Eight images randomly captured from 4 hearts were analyzed in each group. ( I ) qPCR analyses of Nppa and Nppb genes normalized to β-actin. N = 4. All data were analyzed by unpaired 2-tailed Student’s t test. *P
    Figure Legend Snippet: Levels of mtDNA with deletion and tissue ROS were increased in the mdx mouse heart. ( A ) Schematic depicting the regions of the mouse mitochondrial genome (mtDNA) amplified by long-range PCR [nucleotide positions (np) 9984-3577 and np 3553–9990] and the qPCR methods. ( B ) mtDNA content determined by qPCR amplifying the D-loop and COX2 regions and nuclear RPS18 genome region. N = 4. ( C ) Representative gel images of long-range PCR of myocardial DNA samples. For quantification, the results of 10, 5, and 2.5 ng of DNA from an intact mouse heart per reaction were included. The nuclear Gapdh gene was amplified as an internal control. ( D ) Levels of long-range PCR products normalized to Gapdh . N = 4. ( E ) Representative Immunoblots for VDAC1, SDHA, Rieske, HSP60, and GAPDH. ( F ) Levels of mitochondrial proteins in the hearts. ( G ) Dihydroethidium (DHE) fluorescence (red) images in heart sections from 22-week-old control and mdx mice. ( H ) Relative DHE fluorescence intensity. Eight images randomly captured from 4 hearts were analyzed in each group. ( I ) qPCR analyses of Nppa and Nppb genes normalized to β-actin. N = 4. All data were analyzed by unpaired 2-tailed Student’s t test. *P

    Techniques Used: Amplification, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Western Blot, Fluorescence, Mouse Assay

    2) Product Images from "The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer"

    Article Title: The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer

    Journal: Cell Death & Disease

    doi: 10.1038/s41419-017-0137-x

    UBC13 controls DNMT1 stability via ubiquitination and DNMT1 participates in UBC13 regulation of the paclitaxel sensitivity DNMT1 ubiquitination in a A2780 and b SKOV3 cells with UBC13-overexpression or c A2780 and d SKOV3 with UBC13-knockdown without or with HA-ubiquitin. Cells were treated with MG-132 (20 μM, 8 h) prior to preparation of lysates and then subjected to IP followed by western blot with the indicated antibodies. e Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days, and treated with paclitaxel at the indicated concentrations. f Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days. g Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were treated with paclitaxel at the indicated concentrations. h Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown. Results are shown as means ± SEM for at least three separate experiments in ( e and g ) (* P
    Figure Legend Snippet: UBC13 controls DNMT1 stability via ubiquitination and DNMT1 participates in UBC13 regulation of the paclitaxel sensitivity DNMT1 ubiquitination in a A2780 and b SKOV3 cells with UBC13-overexpression or c A2780 and d SKOV3 with UBC13-knockdown without or with HA-ubiquitin. Cells were treated with MG-132 (20 μM, 8 h) prior to preparation of lysates and then subjected to IP followed by western blot with the indicated antibodies. e Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days, and treated with paclitaxel at the indicated concentrations. f Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days. g Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were treated with paclitaxel at the indicated concentrations. h Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown. Results are shown as means ± SEM for at least three separate experiments in ( e and g ) (* P

    Techniques Used: Over Expression, Western Blot, Transfection, shRNA

    3) Product Images from "Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics"

    Article Title: Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2018.10.011

    Epigenetic profile of CAID patients. ( A ) Heatmap representation of methylation levels in CAID patients vs controls among all tiles at early (p8) and late stage (p14) showed a global hypermethylation pattern. ( B ) Volcano plot of the methylation difference (%) at early (p8) and late stage (p14). Yellow ≥-30% and blue ≥30% methylation differences. ( C ) Tile proportions of differentially methylated regions at early (p8) and late stage (p14). For each group, N = 3 independent biological replicates. P values were corrected for multiple testing using the Benjamini–Hochberg method (q value). ( D ) Methylation percentage of LINE-1 CpG sites assessed by pyrosequencing. LINE-1 CpGs are significantly more methylated in CAID patients than in controls. Error bars signify SD. For each condition, the experiment was performed on N = 3 independent biological replicates in technical replicates. Significance was calculated by 1-way analysis of variance with the Bonferroni post-test ( • P
    Figure Legend Snippet: Epigenetic profile of CAID patients. ( A ) Heatmap representation of methylation levels in CAID patients vs controls among all tiles at early (p8) and late stage (p14) showed a global hypermethylation pattern. ( B ) Volcano plot of the methylation difference (%) at early (p8) and late stage (p14). Yellow ≥-30% and blue ≥30% methylation differences. ( C ) Tile proportions of differentially methylated regions at early (p8) and late stage (p14). For each group, N = 3 independent biological replicates. P values were corrected for multiple testing using the Benjamini–Hochberg method (q value). ( D ) Methylation percentage of LINE-1 CpG sites assessed by pyrosequencing. LINE-1 CpGs are significantly more methylated in CAID patients than in controls. Error bars signify SD. For each condition, the experiment was performed on N = 3 independent biological replicates in technical replicates. Significance was calculated by 1-way analysis of variance with the Bonferroni post-test ( • P

    Techniques Used: Methylation

    4) Product Images from "Reappraisal of the Therapeutic Role of Celecoxib in Cholangiocarcinoma"

    Article Title: Reappraisal of the Therapeutic Role of Celecoxib in Cholangiocarcinoma

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0069928

    COX-2 expression in rat CCA and apoptosis detection in treated rat CCA. (A) Rat CCA tissue revealed positive cytoplasmic immunoreactivity for COX-2 (×400). (B) Apoptotic DNA fragmentation of rat CCA tissue after treatment with celecoxib (160 mg/kg body weight) for 5 weeks visualised by the DNA laddering assay. No apoptotic DNA fragmentation was observed in the control group treated with DMSO buffer for 5 weeks. (C, D, E) TUNNEL assay for determination of rat CCA apoptosis. The positive cells for TUNNEL assay with brown stains are shown in the positive control (TACS-Nuclease treated tissues ) figure (D). No apoptosis was detected in the control group (C). (E) Apoptosis cells were detected in rat CCA tissues treated with celecoxib (160 mg/kg body weight).
    Figure Legend Snippet: COX-2 expression in rat CCA and apoptosis detection in treated rat CCA. (A) Rat CCA tissue revealed positive cytoplasmic immunoreactivity for COX-2 (×400). (B) Apoptotic DNA fragmentation of rat CCA tissue after treatment with celecoxib (160 mg/kg body weight) for 5 weeks visualised by the DNA laddering assay. No apoptotic DNA fragmentation was observed in the control group treated with DMSO buffer for 5 weeks. (C, D, E) TUNNEL assay for determination of rat CCA apoptosis. The positive cells for TUNNEL assay with brown stains are shown in the positive control (TACS-Nuclease treated tissues ) figure (D). No apoptosis was detected in the control group (C). (E) Apoptosis cells were detected in rat CCA tissues treated with celecoxib (160 mg/kg body weight).

    Techniques Used: Expressing, DNA Laddering, Positive Control

    5) Product Images from "Rapid Point-of-Care Isothermal Amplification Assay for the Detection of Malaria without Nucleic Acid Purification"

    Article Title: Rapid Point-of-Care Isothermal Amplification Assay for the Detection of Malaria without Nucleic Acid Purification

    Journal: Infectious Diseases

    doi: 10.4137/IDRT.S32162

    LAMP of DNA isolated from DBS showing real-time amplification in the positive control (genomic Plasmodium DNA) and amplification from DNA isolated from DBS containing 10 3 and 10 6 parasites/µL.
    Figure Legend Snippet: LAMP of DNA isolated from DBS showing real-time amplification in the positive control (genomic Plasmodium DNA) and amplification from DNA isolated from DBS containing 10 3 and 10 6 parasites/µL.

    Techniques Used: Isolation, Amplification, Positive Control

    6) Product Images from "Identification of a novel β-adrenergic octopamine receptor-like gene (βAOR-like) and increased ATP-binding cassette B10 (ABCB10) expression in a Rhipicephalus microplus cell line derived from acaricide-resistant ticks"

    Article Title: Identification of a novel β-adrenergic octopamine receptor-like gene (βAOR-like) and increased ATP-binding cassette B10 (ABCB10) expression in a Rhipicephalus microplus cell line derived from acaricide-resistant ticks

    Journal: Parasites & Vectors

    doi: 10.1186/s13071-016-1708-x

    βAOR PCR in Rhipicephalus cell lines. a Detection of βAOR in genomic DNA (gDNA) and complementary DNA (cDNA) of Rhipicephalus microplus cell lines. The expected amplicon of 183 bp was detected in gDNA and cDNA of cell lines BME/CTVM2 (2), BME/CTVM5 (5), BME/CTVM23 (23), BME/CTVM30 (30) and BmVIII-SCC (SCC). BME/CTVM6 (6) gave an alternative amplicon of ~220 bp from both gDNA and cDNA. Additional amplicons of ~245 bp and ~220 bp were also detected in gDNA of BME/CTVM5. b Detection of βAOR in gDNA and cDNA of other tick cell lines. The expected amplicon was detected in gDNA and cDNA of cell lines RAN/CTVM3 (RAN), REN/CTVM32 (REN), RSE/PILS35 (RSE) and RA243, and only in gDNA of RML-RSE (RML). No βAOR gene or transcript was detected in cell lines AVL/CTVM13 (AVL), HAE/CTVM9 (HAE) or IRE/CTVM19 (IRE). Abbreviations : M, Marker; NTC, Non-template control; −ve, reverse transcription negative control
    Figure Legend Snippet: βAOR PCR in Rhipicephalus cell lines. a Detection of βAOR in genomic DNA (gDNA) and complementary DNA (cDNA) of Rhipicephalus microplus cell lines. The expected amplicon of 183 bp was detected in gDNA and cDNA of cell lines BME/CTVM2 (2), BME/CTVM5 (5), BME/CTVM23 (23), BME/CTVM30 (30) and BmVIII-SCC (SCC). BME/CTVM6 (6) gave an alternative amplicon of ~220 bp from both gDNA and cDNA. Additional amplicons of ~245 bp and ~220 bp were also detected in gDNA of BME/CTVM5. b Detection of βAOR in gDNA and cDNA of other tick cell lines. The expected amplicon was detected in gDNA and cDNA of cell lines RAN/CTVM3 (RAN), REN/CTVM32 (REN), RSE/PILS35 (RSE) and RA243, and only in gDNA of RML-RSE (RML). No βAOR gene or transcript was detected in cell lines AVL/CTVM13 (AVL), HAE/CTVM9 (HAE) or IRE/CTVM19 (IRE). Abbreviations : M, Marker; NTC, Non-template control; −ve, reverse transcription negative control

    Techniques Used: Polymerase Chain Reaction, Amplification, Marker, Negative Control

    7) Product Images from "Nuclear Perilipin 5 integrates lipid droplet lipolysis with PGC-1α/SIRT1-dependent transcriptional regulation of mitochondrial function"

    Article Title: Nuclear Perilipin 5 integrates lipid droplet lipolysis with PGC-1α/SIRT1-dependent transcriptional regulation of mitochondrial function

    Journal: Nature Communications

    doi: 10.1038/ncomms12723

    Catecholamine treatment triggers Perilipin 5 interaction with PGC-1α and SIRT1 that promotes PGC-1α deacetylation. ( a ) Immunoprecipitation (IP) of PGC-1α (left) and of Perilipin 5 (right) from nuclear extracts of C2C12 myotubes treated with vehicle or Iso/IBMX for 2 h. ( b ) IP of Perilipin 5 from BAT of wild-type mice treated with β3 adrenergic agonist CL 316,243 (CL) or vehicle. ( c , d ) IP of Perilipin 5 ( c ) or PGC-1α ( d ) from whole-cell lysate of brown adipocytes treated with vehicle or Iso/IBMX for 2 h. IgG control IP and siRNA duplexes for PGC-1α and/or Perilipin 5 were used as IP controls. ( e ) IP from whole-cell extract of C2C12 myoblasts transfected with myc-Perilipin 5 and flag-PGC-1α and treated with Iso/IBMX for 2 h. Non-transfected cells were used as IP control. ( f ) PLA reveals Perilipin 5 interaction with PGC-1α in C2C12 differentiating myoblasts treated with vehicle or Iso/IBMX for 2 h. Red dots indicate proximity of interaction partners within 20–40 nm (left) with quantification using Cell Profiler software (right). ( g ) IP of PGC-1α from whole-cell lysate of brown adypocytes treated with Iso/IBMX for 2 h. Cells were additionally treated with orlistat or vehicle and siATGL or siControl. IgG control and siPGC-1α were used as IP controls. ( h ) IP of PGC-1α from nuclear extracts of MLTC-1 cells transfected with siControl or siPerilipin 5. Non-immune rabbit IgG was used as the IP-negative control.
    Figure Legend Snippet: Catecholamine treatment triggers Perilipin 5 interaction with PGC-1α and SIRT1 that promotes PGC-1α deacetylation. ( a ) Immunoprecipitation (IP) of PGC-1α (left) and of Perilipin 5 (right) from nuclear extracts of C2C12 myotubes treated with vehicle or Iso/IBMX for 2 h. ( b ) IP of Perilipin 5 from BAT of wild-type mice treated with β3 adrenergic agonist CL 316,243 (CL) or vehicle. ( c , d ) IP of Perilipin 5 ( c ) or PGC-1α ( d ) from whole-cell lysate of brown adipocytes treated with vehicle or Iso/IBMX for 2 h. IgG control IP and siRNA duplexes for PGC-1α and/or Perilipin 5 were used as IP controls. ( e ) IP from whole-cell extract of C2C12 myoblasts transfected with myc-Perilipin 5 and flag-PGC-1α and treated with Iso/IBMX for 2 h. Non-transfected cells were used as IP control. ( f ) PLA reveals Perilipin 5 interaction with PGC-1α in C2C12 differentiating myoblasts treated with vehicle or Iso/IBMX for 2 h. Red dots indicate proximity of interaction partners within 20–40 nm (left) with quantification using Cell Profiler software (right). ( g ) IP of PGC-1α from whole-cell lysate of brown adypocytes treated with Iso/IBMX for 2 h. Cells were additionally treated with orlistat or vehicle and siATGL or siControl. IgG control and siPGC-1α were used as IP controls. ( h ) IP of PGC-1α from nuclear extracts of MLTC-1 cells transfected with siControl or siPerilipin 5. Non-immune rabbit IgG was used as the IP-negative control.

    Techniques Used: Pyrolysis Gas Chromatography, Immunoprecipitation, Mouse Assay, Transfection, Proximity Ligation Assay, Software, Negative Control

    Perilipin 5 regulates catecholamine-stimulated SIRT1 deacetylation activity and mitochondrial biogenesis and respiration. ( a ) MLTC-1 cells were transfected with the indicated siRNA duplexes. After 72 h, cells were treated with Iso/IBMX or vehicle for 30 min and SIRT1 deacetylase activity was measured in the cell lysates (left). Western blotting for SIRT1, Perilipin 5 and GAPDH document siRNA specificity (bottom). Intracellular NAD + levels with Iso/IBMX or siPerilipin 5 treatments (right). ( b ) Immunoprecipitation of SIRT1 followed by WB for DBC1 and SIRT1 from MLTC-1 cells transfected with the indicated siRNA duplexes. Cells were treated with vehicle or Iso/IBMX for 30 min before immunoprecipitation. Relative quantification of immunoprecipitated DBC-1 normalized for immunoprecipitated SIRT1 is shown in the histogram. ( c ) PLA for SIRT1-DBC1 complexes (red dots) in MLTC-1 cells transfected with the indicated siRNA duplexes for 48 h followed by treatment with vehicle or Iso/IBMX for 30 min (left) with quantification using Cell Profiler (right). ( d ) mtDNA content analysed by qPCR in brown adipocytes transfected with siControl or siPerilipin 5 followed by treatment with vehicle or Iso/IBMX for 2 h. ( e ) OCR in brown adipocytes transfected with siControl or siPerilipin 5 followed by treatment with vehicle or Iso/IBMX. n =3 biological replicates/experimental condition with each biological replicate representing an independent transfection and treatment. Values are expressed as the mean±s.e.m. These data were replicated in a second independent experiment. * P
    Figure Legend Snippet: Perilipin 5 regulates catecholamine-stimulated SIRT1 deacetylation activity and mitochondrial biogenesis and respiration. ( a ) MLTC-1 cells were transfected with the indicated siRNA duplexes. After 72 h, cells were treated with Iso/IBMX or vehicle for 30 min and SIRT1 deacetylase activity was measured in the cell lysates (left). Western blotting for SIRT1, Perilipin 5 and GAPDH document siRNA specificity (bottom). Intracellular NAD + levels with Iso/IBMX or siPerilipin 5 treatments (right). ( b ) Immunoprecipitation of SIRT1 followed by WB for DBC1 and SIRT1 from MLTC-1 cells transfected with the indicated siRNA duplexes. Cells were treated with vehicle or Iso/IBMX for 30 min before immunoprecipitation. Relative quantification of immunoprecipitated DBC-1 normalized for immunoprecipitated SIRT1 is shown in the histogram. ( c ) PLA for SIRT1-DBC1 complexes (red dots) in MLTC-1 cells transfected with the indicated siRNA duplexes for 48 h followed by treatment with vehicle or Iso/IBMX for 30 min (left) with quantification using Cell Profiler (right). ( d ) mtDNA content analysed by qPCR in brown adipocytes transfected with siControl or siPerilipin 5 followed by treatment with vehicle or Iso/IBMX for 2 h. ( e ) OCR in brown adipocytes transfected with siControl or siPerilipin 5 followed by treatment with vehicle or Iso/IBMX. n =3 biological replicates/experimental condition with each biological replicate representing an independent transfection and treatment. Values are expressed as the mean±s.e.m. These data were replicated in a second independent experiment. * P

    Techniques Used: Activity Assay, Transfection, Histone Deacetylase Assay, Western Blot, Immunoprecipitation, Proximity Ligation Assay, Real-time Polymerase Chain Reaction

    8) Product Images from "The interactions of dopamine and oxidative damage in the striatum of patients with neurodegenerative diseases"

    Article Title: The interactions of dopamine and oxidative damage in the striatum of patients with neurodegenerative diseases

    Journal: Journal of Neurochemistry

    doi: 10.1111/jnc.14898

    (a) Concentration of dopamine in the caudate and putamen from patients with diseases [Parkinson disease (PD): n = 10, Parkinson disease dementia (PDD): n = 7, dementia with Lewy bodies (DLB): n = 10, Alzheimer's disease (AD): n = 26] and age‐matched controls ( n = 10). Value shown are means ± SEM. (b) Concentration of dopamine vs level of 8‐oxo‐7,8‐dihydro‐2'‐deoxyguanosine (8‐oxo‐dG) in the caudate from diseases brains, significantly association was observed only in AD group ( p = 0.026). (c) Concentration of dopamine vs vesicular monoamine transporter 2 (VMAT2) expression in the putamen from diseases brains, significantly association was observed only in DLB group ( p = 0.050). r s , the Spearman's rank correlation coefficient.
    Figure Legend Snippet: (a) Concentration of dopamine in the caudate and putamen from patients with diseases [Parkinson disease (PD): n = 10, Parkinson disease dementia (PDD): n = 7, dementia with Lewy bodies (DLB): n = 10, Alzheimer's disease (AD): n = 26] and age‐matched controls ( n = 10). Value shown are means ± SEM. (b) Concentration of dopamine vs level of 8‐oxo‐7,8‐dihydro‐2'‐deoxyguanosine (8‐oxo‐dG) in the caudate from diseases brains, significantly association was observed only in AD group ( p = 0.026). (c) Concentration of dopamine vs vesicular monoamine transporter 2 (VMAT2) expression in the putamen from diseases brains, significantly association was observed only in DLB group ( p = 0.050). r s , the Spearman's rank correlation coefficient.

    Techniques Used: Concentration Assay, Expressing

    8‐oxo‐dG levels in the caudate and putamen from patients with diseases [Parkinson disease (PD): n = 10, Parkinson disease dementia (PDD): n = 7, dementia with Lewy bodies (DLB): n = 10, Alzheimer's disease (AD): n = 26] and age‐matched controls ( n = 10). Value shown are means ± SEM as the concentration of 8‐oxo‐7,8‐dihydro‐2'‐deoxyguanosine (8‐oxo‐dG) (pg) per total DNA (µg). A p value of
    Figure Legend Snippet: 8‐oxo‐dG levels in the caudate and putamen from patients with diseases [Parkinson disease (PD): n = 10, Parkinson disease dementia (PDD): n = 7, dementia with Lewy bodies (DLB): n = 10, Alzheimer's disease (AD): n = 26] and age‐matched controls ( n = 10). Value shown are means ± SEM as the concentration of 8‐oxo‐7,8‐dihydro‐2'‐deoxyguanosine (8‐oxo‐dG) (pg) per total DNA (µg). A p value of

    Techniques Used: Concentration Assay

    9) Product Images from "Distinct Role of Sesn2 in Response to UVB-Induced DNA Damage and UVA-Induced Oxidative Stress in Melanocytes †"

    Article Title: Distinct Role of Sesn2 in Response to UVB-Induced DNA Damage and UVA-Induced Oxidative Stress in Melanocytes †

    Journal: Photochemistry and photobiology

    doi: 10.1111/php.12624

    Role of Sesn2 in UVB-induced DNA damage repair. (A) Slot blot analysis of CPD levels in A375 cells stably infected with plu-GFP (control) or plu-Sesn2 at 0, 20 h or 48 h post-UVB irradiation. (B) Quantification of A. (C) Slot blot analysis of CPD levels
    Figure Legend Snippet: Role of Sesn2 in UVB-induced DNA damage repair. (A) Slot blot analysis of CPD levels in A375 cells stably infected with plu-GFP (control) or plu-Sesn2 at 0, 20 h or 48 h post-UVB irradiation. (B) Quantification of A. (C) Slot blot analysis of CPD levels

    Techniques Used: Dot Blot, Stable Transfection, Infection, Irradiation

    10) Product Images from "Rapid pathogen identification using a novel microarray-based assay with purulent meningitis in cerebrospinal fluid"

    Article Title: Rapid pathogen identification using a novel microarray-based assay with purulent meningitis in cerebrospinal fluid

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-34051-0

    The specificity and sensitivity of the pathogen probes. ( A ) Microarray hybridized with the probe untarget bacteria and human genome DNA. ( B ) Microarray hybridized with the probe target bacteria. NC means microarray hybridized with ddH 2 O and positive control sequence (show the signal of PC probes). ( C ) Microarray hybridized with the Escherichia coli (ATCC 25922) which diluted for concentration gradient (the original DNA samples were extracted from CSF).
    Figure Legend Snippet: The specificity and sensitivity of the pathogen probes. ( A ) Microarray hybridized with the probe untarget bacteria and human genome DNA. ( B ) Microarray hybridized with the probe target bacteria. NC means microarray hybridized with ddH 2 O and positive control sequence (show the signal of PC probes). ( C ) Microarray hybridized with the Escherichia coli (ATCC 25922) which diluted for concentration gradient (the original DNA samples were extracted from CSF).

    Techniques Used: Microarray, Positive Control, Sequencing, Concentration Assay

    11) Product Images from "Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells"

    Article Title: Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells

    Journal: Oncotarget

    doi: 10.18632/oncotarget.10701

    Plots of CNA profiles along the whole genome (x axis) ( A ) CNA profile of unamplified DNA from unfixed cells. ( B – G ) plots of CNAs in single SK-BR-3 cells, obtained from EDTA-preserved blood. ( H , I ) CNA profiles of individual CTCs, obtained from EDTA-preserved blood of the same breast cancer patient. WGA kits: (B, E) Ampli1; (C, F, H, I) PicoPlex; (D, G) REPLI-g.
    Figure Legend Snippet: Plots of CNA profiles along the whole genome (x axis) ( A ) CNA profile of unamplified DNA from unfixed cells. ( B – G ) plots of CNAs in single SK-BR-3 cells, obtained from EDTA-preserved blood. ( H , I ) CNA profiles of individual CTCs, obtained from EDTA-preserved blood of the same breast cancer patient. WGA kits: (B, E) Ampli1; (C, F, H, I) PicoPlex; (D, G) REPLI-g.

    Techniques Used: Whole Genome Amplification

    Distribution of identified known SNPs between datasets ( A ) Known SNPs identified in single cells, amplified with Ampli1, PicoPlex, and REPLI-g WGA kits and obtained from EDTA-preserved blood in comparison to unamplified DNA. ( B ) Known SNPs identified in single cells, amplified with Ampli1 or PicoPlex and obtained from EDTA- and CellSave-preserved blood in comparison to unamplified DNA from unfixed cells. ( C ) Known SNPs identified in single CTCs, amplified with PicoPlex in comparison to each other.
    Figure Legend Snippet: Distribution of identified known SNPs between datasets ( A ) Known SNPs identified in single cells, amplified with Ampli1, PicoPlex, and REPLI-g WGA kits and obtained from EDTA-preserved blood in comparison to unamplified DNA. ( B ) Known SNPs identified in single cells, amplified with Ampli1 or PicoPlex and obtained from EDTA- and CellSave-preserved blood in comparison to unamplified DNA from unfixed cells. ( C ) Known SNPs identified in single CTCs, amplified with PicoPlex in comparison to each other.

    Techniques Used: Amplification, Whole Genome Amplification

    12) Product Images from "Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples"

    Article Title: Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

    Journal: Biopreservation and Biobanking

    doi: 10.1089/bio.2011.0034

    (A, B) Qubit DNA yields for fresh frozen tumor tissue (*), Fresh frozen normal tissue (**), Allprotect-treated tumor tissue, and Allprotect-treated normal tissue isolated using (A) Qiagen's QIAamp kit (B) Qiagen's AllPrep kit.
    Figure Legend Snippet: (A, B) Qubit DNA yields for fresh frozen tumor tissue (*), Fresh frozen normal tissue (**), Allprotect-treated tumor tissue, and Allprotect-treated normal tissue isolated using (A) Qiagen's QIAamp kit (B) Qiagen's AllPrep kit.

    Techniques Used: Isolation

    DNA isolation using the QIAamp Kit
    Figure Legend Snippet: DNA isolation using the QIAamp Kit

    Techniques Used: DNA Extraction

    13) Product Images from "Toxigenic properties and stx phage characterization of Escherichia coli O157 isolated from animal sources in a developing country setting"

    Article Title: Toxigenic properties and stx phage characterization of Escherichia coli O157 isolated from animal sources in a developing country setting

    Journal: BMC Microbiology

    doi: 10.1186/s12866-018-1235-3

    Field inversion gel electrophoresis (FIGE) analysis of phage DNA. (A1) FIGE analysis of Eco RI- digested phage DNA induced from toxin-producing E. coli O157 isolates and (A2) its corresponding blot hybridized with radioactively labeled stx 2 probe. Lane 1: M18 (undigested), Lane 2: M18 (digested), Lane 3: M133 (undigested), Lane 4: M133 (digested), Lane 5: 1 kb Marker, Lane 6: M163 (undigested), Lane 7: M163 (digested), Lane 8: G51 (undigested), Lane 9: G51 (digested), Lane 10: G71 (undigested), Lane 11: G71 (digested). (B1) FIGE analysis of phage DNA induced and uninduced from toxin-producing E. coli O157 isolates and (B2) its corresponding blot hybridized with radioactively labeled stx 2 probe. Lane 1: M18 (uninduced), Lane 2: M18 (induced), Lane 3: M133 (uninduced), Lane 4: M133 (induced), Lane 5: G71 (uninduced), Lane 6: G71 (induced), Lane 7: M163 (uninduced), Lane 8: M163 (induced), Lane 9: G51 (uninduced), Lane 10: G51 (induced). (C1) FIGE analysis of phage DNA induced and uninduced from E. coli O157 isolates producing little or no toxin and (C2) its corresponding blot hybridized with radioactively labeled stx 2 probe. Lane 1: C96 (uninduced), Lane 2: C96 (induced), Lane 3: M143 (uninduced), Lane 4: M143 (induced), Lane 5: M168 (uninduced), Lane 6: M168 (induced), Lane 7: M171 (uninduced), Lane 8: M171 (induced), Lane 9: M173 (uninduced), Lane 10: M173 (induced)
    Figure Legend Snippet: Field inversion gel electrophoresis (FIGE) analysis of phage DNA. (A1) FIGE analysis of Eco RI- digested phage DNA induced from toxin-producing E. coli O157 isolates and (A2) its corresponding blot hybridized with radioactively labeled stx 2 probe. Lane 1: M18 (undigested), Lane 2: M18 (digested), Lane 3: M133 (undigested), Lane 4: M133 (digested), Lane 5: 1 kb Marker, Lane 6: M163 (undigested), Lane 7: M163 (digested), Lane 8: G51 (undigested), Lane 9: G51 (digested), Lane 10: G71 (undigested), Lane 11: G71 (digested). (B1) FIGE analysis of phage DNA induced and uninduced from toxin-producing E. coli O157 isolates and (B2) its corresponding blot hybridized with radioactively labeled stx 2 probe. Lane 1: M18 (uninduced), Lane 2: M18 (induced), Lane 3: M133 (uninduced), Lane 4: M133 (induced), Lane 5: G71 (uninduced), Lane 6: G71 (induced), Lane 7: M163 (uninduced), Lane 8: M163 (induced), Lane 9: G51 (uninduced), Lane 10: G51 (induced). (C1) FIGE analysis of phage DNA induced and uninduced from E. coli O157 isolates producing little or no toxin and (C2) its corresponding blot hybridized with radioactively labeled stx 2 probe. Lane 1: C96 (uninduced), Lane 2: C96 (induced), Lane 3: M143 (uninduced), Lane 4: M143 (induced), Lane 5: M168 (uninduced), Lane 6: M168 (induced), Lane 7: M171 (uninduced), Lane 8: M171 (induced), Lane 9: M173 (uninduced), Lane 10: M173 (induced)

    Techniques Used: Nucleic Acid Electrophoresis, Labeling, Marker

    Detection of integration of stx 2 phage DNA with E. coli MC1061 chromosome by PFGE analysis. Lane 1: Salmonella Braenderup, Lane 2: E. coli O157 G51, Lane 3: E. coli MC1061, Lane 4: E. coli MC1061-Lysogen. The bottom arrow mark denotes the position of the band in E. coli MC1061 which is missing in all lysogenic strains of E. coli MC1061. The arrow mark above denotes the intensity of a band in all lysogenic strains of E. coli MC1061 which is significantly higher than that of the non-lysogenic E. coli MC1061 strain
    Figure Legend Snippet: Detection of integration of stx 2 phage DNA with E. coli MC1061 chromosome by PFGE analysis. Lane 1: Salmonella Braenderup, Lane 2: E. coli O157 G51, Lane 3: E. coli MC1061, Lane 4: E. coli MC1061-Lysogen. The bottom arrow mark denotes the position of the band in E. coli MC1061 which is missing in all lysogenic strains of E. coli MC1061. The arrow mark above denotes the intensity of a band in all lysogenic strains of E. coli MC1061 which is significantly higher than that of the non-lysogenic E. coli MC1061 strain

    Techniques Used:

    14) Product Images from "Inhibition of LCMR1 and ATG12 by demethylation-activated miR-570-3p is involved in the anti-metastasis effects of metformin on human osteosarcoma"

    Article Title: Inhibition of LCMR1 and ATG12 by demethylation-activated miR-570-3p is involved in the anti-metastasis effects of metformin on human osteosarcoma

    Journal: Cell Death & Disease

    doi: 10.1038/s41419-018-0620-z

    Metformin up-regulates the expression of miR-570-3p by the demethylation of DNA in 143B and U2OS cells. a The CpG islands of miR-570-3p promoter regions and primer used for DNA methylation study. b Metformin treatment in 143B and U2OS cells significantly decreased DNA methylation levels at the CpG islands of miR-570-3p promoter regions
    Figure Legend Snippet: Metformin up-regulates the expression of miR-570-3p by the demethylation of DNA in 143B and U2OS cells. a The CpG islands of miR-570-3p promoter regions and primer used for DNA methylation study. b Metformin treatment in 143B and U2OS cells significantly decreased DNA methylation levels at the CpG islands of miR-570-3p promoter regions

    Techniques Used: Expressing, DNA Methylation Assay

    15) Product Images from "Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid"

    Article Title: Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-22416-4

    Sample collection, DNA isolation and shotgun metagenomic sequencing. ( A ) (I.) Sample collection: Vitreous body (intraocular body fluid) was collected through vitrectomy from 14 patients with endophthalmitis following cataract surgery (n = 7) and intravitreal injection (n = 7). As control, vitreous was collected from 7 patients without postoperative endophthalmitis during macula hole surgery. Six aliquots (3 sample pairs) were obtained from balanced salt solution (BSS) that is infused into the eye during vitrectomy. Three aliquots were collected from separate BSS bottles (BSS-B) and the second set of aliquots was collected from the vitrectomy surgical system (BSS-S) after it had passed through the vitrectomy infusion line, respectively. The samples were examined using (II.) Cultivation-based analyses and (III.) DNA isolation (2 methods) Metagenomic shotgun sequencing, including the examination of DNA extraction (blank) controls. A total of 62 samples were sequenced using Illumina MiSeq sequencing technology. ( B ) More details to steps (II.) and (III.): (II.) Cultivation-based analyses: Aliquots of the vitreous body fluid and balanced salt solution samples were subjected to cultivation-based analyses separately at the hospital and research laboratories. Obtained isolates were analyzed using mass spectrometry and whole genome sequencing. (III.) DNA isolation Metagenomic shotgun sequencing: Samples were extracted using two DNA isolation procedures: QIAamp DNA Mini Kit (QIA) and QIAamp UCP Pathogen Mini kit (UCP). A DNA extraction (blank) control was included at each round of DNA isolation, i.e. one DNA extraction control for 12–14 samples in total per extraction round (more vitreous samples were extracted than analyzed in this study). To verify the presence of the main microorganisms detected in the metagenomics analysis, the shotgun metagenomics reads were mapped to the genome assemblies of the isolates obtained from the vitreous samples. Not displayed here is the mapping of metagenomic shotgun reads to microbial reference genomes in the database (Provided in Fig. 4 ). As an additional verification, PCR analyses were carried out to detect the presence of the most abundant microorganisms in the vitreous samples using organism-specific primer sets.
    Figure Legend Snippet: Sample collection, DNA isolation and shotgun metagenomic sequencing. ( A ) (I.) Sample collection: Vitreous body (intraocular body fluid) was collected through vitrectomy from 14 patients with endophthalmitis following cataract surgery (n = 7) and intravitreal injection (n = 7). As control, vitreous was collected from 7 patients without postoperative endophthalmitis during macula hole surgery. Six aliquots (3 sample pairs) were obtained from balanced salt solution (BSS) that is infused into the eye during vitrectomy. Three aliquots were collected from separate BSS bottles (BSS-B) and the second set of aliquots was collected from the vitrectomy surgical system (BSS-S) after it had passed through the vitrectomy infusion line, respectively. The samples were examined using (II.) Cultivation-based analyses and (III.) DNA isolation (2 methods) Metagenomic shotgun sequencing, including the examination of DNA extraction (blank) controls. A total of 62 samples were sequenced using Illumina MiSeq sequencing technology. ( B ) More details to steps (II.) and (III.): (II.) Cultivation-based analyses: Aliquots of the vitreous body fluid and balanced salt solution samples were subjected to cultivation-based analyses separately at the hospital and research laboratories. Obtained isolates were analyzed using mass spectrometry and whole genome sequencing. (III.) DNA isolation Metagenomic shotgun sequencing: Samples were extracted using two DNA isolation procedures: QIAamp DNA Mini Kit (QIA) and QIAamp UCP Pathogen Mini kit (UCP). A DNA extraction (blank) control was included at each round of DNA isolation, i.e. one DNA extraction control for 12–14 samples in total per extraction round (more vitreous samples were extracted than analyzed in this study). To verify the presence of the main microorganisms detected in the metagenomics analysis, the shotgun metagenomics reads were mapped to the genome assemblies of the isolates obtained from the vitreous samples. Not displayed here is the mapping of metagenomic shotgun reads to microbial reference genomes in the database (Provided in Fig. 4 ). As an additional verification, PCR analyses were carried out to detect the presence of the most abundant microorganisms in the vitreous samples using organism-specific primer sets.

    Techniques Used: DNA Extraction, Sequencing, Injection, Shotgun Sequencing, Mass Spectrometry, Polymerase Chain Reaction

    Summary of cultivation-based, metagenomics and whole genome sequence analyses. Bacterial isolates were obtained at the hospital laboratory (1 st cultivation) from vitreous from endophthalmitis patients following cataract surgery (C1-7) and intravitreal injection (I1-7) and the taxonomic affiliation of the isolates were determined by MALDI-TOF mass spectrometry (MS). Vitreous was analyzed through metagenomics at the research laboratory using two DNA isolation methods (QIAamp DNA Mini Kit, QIA; QIAamp UCP Pathogen Mini kit, UCP) and the taxonomic affiliation of reads was determined. The detected amount of human DNA sequences in percent (%) is provided in the first column of the Metagenomics tab. In the horizontal bar charts, the taxonomic identity and relative fraction of microbial reads for the most abundant identified organisms based on the Kraken + Bracken analysis is indicated for both DNA isolation methods. The read counts for the most abundant organism according to the Kraken + Bracken (all reads) and BLASTN (forward read) analyses are indicated to the right. The read counts for the most abundant organisms per sample as determined by Kraken, Bracken and BLASTn analyses are available through figshare at https://figshare.com/s/5feabfad1d8c495bf7a3 . Bacterial isolates for some samples were obtained in a second round of cultivation at the research laboratory (2 nd cultivation) and one representative per colony morphotype per vitreous sample was subjected to MS and whole genome sequencing (WGS). The taxonomic affiliation of isolates was determined through classification of assembled genomes using a k-mer based approach and genomic MLST, and antibiotic resistance genes were identified using ResFinder. Furthermore, metagenomic assemblies were generated from the shotgun metagenomic reads and analyzed with regards to taxonomic affiliation and selected functional characteristics (Supplementary Table S6 ). A video summary is available from figshare at https://figshare.com/s/38fe043f6a8ef1710444 .
    Figure Legend Snippet: Summary of cultivation-based, metagenomics and whole genome sequence analyses. Bacterial isolates were obtained at the hospital laboratory (1 st cultivation) from vitreous from endophthalmitis patients following cataract surgery (C1-7) and intravitreal injection (I1-7) and the taxonomic affiliation of the isolates were determined by MALDI-TOF mass spectrometry (MS). Vitreous was analyzed through metagenomics at the research laboratory using two DNA isolation methods (QIAamp DNA Mini Kit, QIA; QIAamp UCP Pathogen Mini kit, UCP) and the taxonomic affiliation of reads was determined. The detected amount of human DNA sequences in percent (%) is provided in the first column of the Metagenomics tab. In the horizontal bar charts, the taxonomic identity and relative fraction of microbial reads for the most abundant identified organisms based on the Kraken + Bracken analysis is indicated for both DNA isolation methods. The read counts for the most abundant organism according to the Kraken + Bracken (all reads) and BLASTN (forward read) analyses are indicated to the right. The read counts for the most abundant organisms per sample as determined by Kraken, Bracken and BLASTn analyses are available through figshare at https://figshare.com/s/5feabfad1d8c495bf7a3 . Bacterial isolates for some samples were obtained in a second round of cultivation at the research laboratory (2 nd cultivation) and one representative per colony morphotype per vitreous sample was subjected to MS and whole genome sequencing (WGS). The taxonomic affiliation of isolates was determined through classification of assembled genomes using a k-mer based approach and genomic MLST, and antibiotic resistance genes were identified using ResFinder. Furthermore, metagenomic assemblies were generated from the shotgun metagenomic reads and analyzed with regards to taxonomic affiliation and selected functional characteristics (Supplementary Table S6 ). A video summary is available from figshare at https://figshare.com/s/38fe043f6a8ef1710444 .

    Techniques Used: Sequencing, Injection, Mass Spectrometry, DNA Extraction, Generated, Functional Assay

    16) Product Images from "Detection of Clostridium botulinum group III in environmental samples from farms by real-time PCR using four commercial DNA extraction kits"

    Article Title: Detection of Clostridium botulinum group III in environmental samples from farms by real-time PCR using four commercial DNA extraction kits

    Journal: BMC Research Notes

    doi: 10.1186/s13104-018-3549-5

    Number of samples in which C. botulinum group III was detected using real-time PCR according to the DNA extraction kit used and the analyzed matrix. Total: number of samples analyzed per matrix. QA QIAamp ® DNA Mini Kit (QIAGEN Inc., Valencia, CA, USA), QF QIAamp ® Fast DNA Stool Mini Kit (QIAGEN Inc., Valencia, CA, USA), PS PowerSoil ® DNA isolation kit (Mo Bio Laboratories Inc., Carlsbad, CA, USA), NS NucleoSpin ® Soil (Macherey–Nagel, Duren, Germany)
    Figure Legend Snippet: Number of samples in which C. botulinum group III was detected using real-time PCR according to the DNA extraction kit used and the analyzed matrix. Total: number of samples analyzed per matrix. QA QIAamp ® DNA Mini Kit (QIAGEN Inc., Valencia, CA, USA), QF QIAamp ® Fast DNA Stool Mini Kit (QIAGEN Inc., Valencia, CA, USA), PS PowerSoil ® DNA isolation kit (Mo Bio Laboratories Inc., Carlsbad, CA, USA), NS NucleoSpin ® Soil (Macherey–Nagel, Duren, Germany)

    Techniques Used: Real-time Polymerase Chain Reaction, DNA Extraction

    17) Product Images from "Comparison of three rapid and easy bacterial DNA extraction methods for use with quantitative real-time PCR"

    Article Title: Comparison of three rapid and easy bacterial DNA extraction methods for use with quantitative real-time PCR

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    doi: 10.1007/s10096-011-1191-4

    DNA extraction efficiencies of the three methods. Percentage of DNA extraction efficiency ( n = 12) of FTA® Elute, the Reischl et al. method and QIAamp® DNA Mini Kit for ( a ) E. coli ATCC 11775 T and ( b ) S. aureus subsp. aureus ATCC 25923. The horizontal bars show the median and quartiles
    Figure Legend Snippet: DNA extraction efficiencies of the three methods. Percentage of DNA extraction efficiency ( n = 12) of FTA® Elute, the Reischl et al. method and QIAamp® DNA Mini Kit for ( a ) E. coli ATCC 11775 T and ( b ) S. aureus subsp. aureus ATCC 25923. The horizontal bars show the median and quartiles

    Techniques Used: DNA Extraction

    Inhibition of the E. coli uidA qrtPCR assay. The mean levels of DNA were determined with qrtPCR by adding a template of 1 ng of the standard together with either water or an extraction control of one of the three following DNA extraction methods to triplicate reactions ( n = 3): FTA® Elute, the Reischl et al. method and QIAamp® DNA Mini Kit. The dashed line represents part of the standard curve. (Ο) FTA® Elute, (□) QIAamp® DNA Mini Kit, (◊) Reischl, (Δ) Water
    Figure Legend Snippet: Inhibition of the E. coli uidA qrtPCR assay. The mean levels of DNA were determined with qrtPCR by adding a template of 1 ng of the standard together with either water or an extraction control of one of the three following DNA extraction methods to triplicate reactions ( n = 3): FTA® Elute, the Reischl et al. method and QIAamp® DNA Mini Kit. The dashed line represents part of the standard curve. (Ο) FTA® Elute, (□) QIAamp® DNA Mini Kit, (◊) Reischl, (Δ) Water

    Techniques Used: Inhibition, DNA Extraction

    DNA levels extracted by three methods with varying amounts of cells. Median DNA levels as determined by qrtPCR resulting from quadruplicate extractions ( n = 4) of different amounts of cells of ( a ) E. coli ATCC 11775 T and ( b ) S. aureus subsp. aureus ATCC 25923. Extractions were performed by three different DNA extraction methods: FTA® Elute, the Reischl et al. method and QIAamp® DNA Mini Kit. The error bars indicate minimum and maximum values. Extrapolated quantification limits of the methods are represented by dotted lines: - - -, FTA® Elute; ─ ─ ─, Reischl et al. and QIAamp® DNA Mini Kit
    Figure Legend Snippet: DNA levels extracted by three methods with varying amounts of cells. Median DNA levels as determined by qrtPCR resulting from quadruplicate extractions ( n = 4) of different amounts of cells of ( a ) E. coli ATCC 11775 T and ( b ) S. aureus subsp. aureus ATCC 25923. Extractions were performed by three different DNA extraction methods: FTA® Elute, the Reischl et al. method and QIAamp® DNA Mini Kit. The error bars indicate minimum and maximum values. Extrapolated quantification limits of the methods are represented by dotted lines: - - -, FTA® Elute; ─ ─ ─, Reischl et al. and QIAamp® DNA Mini Kit

    Techniques Used: DNA Extraction

    18) Product Images from "Leukocyte telomere length variation due to DNA extraction method"

    Article Title: Leukocyte telomere length variation due to DNA extraction method

    Journal: BMC Research Notes

    doi: 10.1186/1756-0500-7-877

    DNA extraction method impacts leukocyte telomere length (T/S ratio). Bars are mean telomere length and error bars are standard deviations. DNA was extracted using the Purelink, QiaAmp and Lahiri and Nurnberger methods, respectively. ** P = 0.003.
    Figure Legend Snippet: DNA extraction method impacts leukocyte telomere length (T/S ratio). Bars are mean telomere length and error bars are standard deviations. DNA was extracted using the Purelink, QiaAmp and Lahiri and Nurnberger methods, respectively. ** P = 0.003.

    Techniques Used: DNA Extraction

    19) Product Images from "Detection of the Agent of Heartwater, Cowdria ruminantium, in Amblyomma Ticks by PCR: Validation and Application of the Assay to Field Ticks"

    Article Title: Detection of the Agent of Heartwater, Cowdria ruminantium, in Amblyomma Ticks by PCR: Validation and Application of the Assay to Field Ticks

    Journal: Journal of Clinical Microbiology

    doi:

    Specificity of the C. ruminantium pCS20 PCR assay against E. chaffeensis . Agarose gel electrophoresis of products from PCRs with C. ruminantium primers and C. ruminantium DNA (lanes 2 and 3) or E. chaffeensis DNA (lanes 4 and 5), with E. chaffeensis primers and C. ruminantium DNA (lanes 8 and 9) or E. chaffeensis DNA (lanes 10 and 11), and with general Ehrlichia primers and C. ruminantium DNA (lanes 14 and 15) or E. chaffeensis DNA (lanes 16 and 17). The 123-bp DNA standard ladder and negative-control reactions for the C. ruminantium , E. chaffeensis , and general Ehrlichia primers are shown in lanes L, 1, 7, and 13, respectively. Lanes 6 and 12 are empty.
    Figure Legend Snippet: Specificity of the C. ruminantium pCS20 PCR assay against E. chaffeensis . Agarose gel electrophoresis of products from PCRs with C. ruminantium primers and C. ruminantium DNA (lanes 2 and 3) or E. chaffeensis DNA (lanes 4 and 5), with E. chaffeensis primers and C. ruminantium DNA (lanes 8 and 9) or E. chaffeensis DNA (lanes 10 and 11), and with general Ehrlichia primers and C. ruminantium DNA (lanes 14 and 15) or E. chaffeensis DNA (lanes 16 and 17). The 123-bp DNA standard ladder and negative-control reactions for the C. ruminantium , E. chaffeensis , and general Ehrlichia primers are shown in lanes L, 1, 7, and 13, respectively. Lanes 6 and 12 are empty.

    Techniques Used: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Negative Control

    20) Product Images from "The effect of deoxyribonucleic acid extraction methods from lymphoid tissue on the purity, content, and amplifying ability"

    Article Title: The effect of deoxyribonucleic acid extraction methods from lymphoid tissue on the purity, content, and amplifying ability

    Journal: Nigerian Medical Journal : Journal of the Nigeria Medical Association

    doi: 10.4103/0300-1652.188321

    5 different extraction methods for three sizes, (a) Figure: 110 bp size, (b) 256 and (c) 512bp of amplified β-globin gene primers. 1. Phenol-chloroform method, 2. QIAamp DNA FFPE Tissue Kit method, 3. Proteinase K and xylol method, 4. Heat alkaline method, 5. Heat alkaline plus mineral oil method and 6 is Negative control
    Figure Legend Snippet: 5 different extraction methods for three sizes, (a) Figure: 110 bp size, (b) 256 and (c) 512bp of amplified β-globin gene primers. 1. Phenol-chloroform method, 2. QIAamp DNA FFPE Tissue Kit method, 3. Proteinase K and xylol method, 4. Heat alkaline method, 5. Heat alkaline plus mineral oil method and 6 is Negative control

    Techniques Used: Amplification, Formalin-fixed Paraffin-Embedded, Negative Control

    21) Product Images from "Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities"

    Article Title: Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0169877

    Normalised DNA yield (ng/ μ L) from (A) plaque and (B) saliva (mean ± SEM). M: MoBio PowerSoil ® DNA Isolation Kit, Q: QIAamp ® DNA Mini Kit, Z: Zymo Bacterial/Fungal DNA Mini Prep TM , P: Phenol:chloroform-based DNA isolation. DNA extraction methods not linked by the same letter are significantly different to each other (Tukey-Kramer p ≤ 0.05).
    Figure Legend Snippet: Normalised DNA yield (ng/ μ L) from (A) plaque and (B) saliva (mean ± SEM). M: MoBio PowerSoil ® DNA Isolation Kit, Q: QIAamp ® DNA Mini Kit, Z: Zymo Bacterial/Fungal DNA Mini Prep TM , P: Phenol:chloroform-based DNA isolation. DNA extraction methods not linked by the same letter are significantly different to each other (Tukey-Kramer p ≤ 0.05).

    Techniques Used: DNA Extraction

    Taxa plots summarising the relative abundance of taxon-assigned OTUs identified in pooled homogenates for (A) bacterial genera in plaque; (B) fungal genera in plaque; (C) bacterial genera in saliva and (D) fungal genera in saliva. Each bar represents sequencing from three replicates, rarefied to 6000 sequences per sample for bacterial genera and 959 for fungal genera, with replicates that did not meet these criteria excluded. M: MoBio PowerSoil ® DNA Isolation Kit, Q: QIAamp ® DNA Mini Kit, Z: Zymo Bacterial/Fungal DNA Mini Prep TM , P: Phenol:chloroform-based DNA isolation.
    Figure Legend Snippet: Taxa plots summarising the relative abundance of taxon-assigned OTUs identified in pooled homogenates for (A) bacterial genera in plaque; (B) fungal genera in plaque; (C) bacterial genera in saliva and (D) fungal genera in saliva. Each bar represents sequencing from three replicates, rarefied to 6000 sequences per sample for bacterial genera and 959 for fungal genera, with replicates that did not meet these criteria excluded. M: MoBio PowerSoil ® DNA Isolation Kit, Q: QIAamp ® DNA Mini Kit, Z: Zymo Bacterial/Fungal DNA Mini Prep TM , P: Phenol:chloroform-based DNA isolation.

    Techniques Used: Sequencing, DNA Extraction

    22) Product Images from "Quantification of Plasmid Copy Number with Single Colour Droplet Digital PCR"

    Article Title: Quantification of Plasmid Copy Number with Single Colour Droplet Digital PCR

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0169846

    Efficiency of genomic and plasmid DNA recovery with the QIAamp DNA mini kit columns. Genomic and plasmid DNA were isolated from E . coli DH5α and E . coli DH5α [pBR322] with the use of Genomic and Plasmid DNA mini kits, respectively (A A Biotechnology). DNA concentrations were measured by NanoDrop 1000 UV-VIS spectrophotometer (Thermo Scientific). Genomic DNA in the following amounts: 2110 ng, 1855 ng and 3922 ng, was coupled with 524 ng, 1100 ng and 1684 ng of plasmid DNA, respectively. Then, 100 μl of the lysis buffer (Qiagen) was added separately to genomic and plasmid DNA and the nucleic acids isolation was performed according to the QIAamp DNA mini kit manufacturer’s manual. The level of isolated DNA is indicated as a percentage relative to the unprocessed sample. The diagram represents three independent experiments. Error bars represent standard deviation (n = 3); (* P
    Figure Legend Snippet: Efficiency of genomic and plasmid DNA recovery with the QIAamp DNA mini kit columns. Genomic and plasmid DNA were isolated from E . coli DH5α and E . coli DH5α [pBR322] with the use of Genomic and Plasmid DNA mini kits, respectively (A A Biotechnology). DNA concentrations were measured by NanoDrop 1000 UV-VIS spectrophotometer (Thermo Scientific). Genomic DNA in the following amounts: 2110 ng, 1855 ng and 3922 ng, was coupled with 524 ng, 1100 ng and 1684 ng of plasmid DNA, respectively. Then, 100 μl of the lysis buffer (Qiagen) was added separately to genomic and plasmid DNA and the nucleic acids isolation was performed according to the QIAamp DNA mini kit manufacturer’s manual. The level of isolated DNA is indicated as a percentage relative to the unprocessed sample. The diagram represents three independent experiments. Error bars represent standard deviation (n = 3); (* P

    Techniques Used: Plasmid Preparation, Isolation, Spectrophotometry, Lysis, Standard Deviation

    Quantification of pBR322 plasmid copy number by digital droplet PCR. E . coli DH5α total DNA isolated by the bead beating method (A) and the QIAamp DNA mini kit (B), from two independent bacterial cultures in a logarithmic growth phase (Experiment 1 and 2), served as a template for the bla and dxs ddPCR amplification with the use of primer set A ( Table 1A ). Each experiment was run in two replicates (bla1, bla2 and dxs1, dxs2). Error bars indicate the 95% confidence limits as determined from the Poisson distribution. (C) Columns A01 and E01 represents single wells of ~ 20,000 droplets after ddPCR amplification of bla and dxs , respectively. (D) Estimated pBR322 copy number by digital droplet PCR. The plasmid copy number of pBR322 was calculated by dividing the copy number of bla by the copy number of dxs . Average PCN from four measurements was determined to be 20.5 for QIA and 7.3 for the bead-beating method.
    Figure Legend Snippet: Quantification of pBR322 plasmid copy number by digital droplet PCR. E . coli DH5α total DNA isolated by the bead beating method (A) and the QIAamp DNA mini kit (B), from two independent bacterial cultures in a logarithmic growth phase (Experiment 1 and 2), served as a template for the bla and dxs ddPCR amplification with the use of primer set A ( Table 1A ). Each experiment was run in two replicates (bla1, bla2 and dxs1, dxs2). Error bars indicate the 95% confidence limits as determined from the Poisson distribution. (C) Columns A01 and E01 represents single wells of ~ 20,000 droplets after ddPCR amplification of bla and dxs , respectively. (D) Estimated pBR322 copy number by digital droplet PCR. The plasmid copy number of pBR322 was calculated by dividing the copy number of bla by the copy number of dxs . Average PCN from four measurements was determined to be 20.5 for QIA and 7.3 for the bead-beating method.

    Techniques Used: Plasmid Preparation, Polymerase Chain Reaction, Isolation, Amplification

    23) Product Images from "Quantitative PCR-Based Measurement of Nuclear and Mitochondrial DNA Damage and Repair in Mammalian Cells"

    Article Title: Quantitative PCR-Based Measurement of Nuclear and Mitochondrial DNA Damage and Repair in Mammalian Cells

    Journal: Methods in molecular biology (Clifton, N.J.)

    doi: 10.1007/978-1-62703-739-6_31

    PCR products of QIAcube-extracted mouse DNA+/−digestion with HaeII. QIAcube extraction apparently results in mostly covalently closed supercoiled mtDNA, which limits primer access. HaeII digestion near the D-Loop (bp ~2,607) greatly increases amplification of the large target. Raw fluorescence values of Lmito ( a ) and Smito ( b ) and hence lesion frequencies ( c ) are affected by digestion. Lesion frequencies represent the decrease in amplification of the large mitochondrial fragment normalized to the small fragment. Data represent the mean+/−SD of two biological samples. Net fluorescence: Picogreen fluorescence of the PCR product minus a “no-template” control
    Figure Legend Snippet: PCR products of QIAcube-extracted mouse DNA+/−digestion with HaeII. QIAcube extraction apparently results in mostly covalently closed supercoiled mtDNA, which limits primer access. HaeII digestion near the D-Loop (bp ~2,607) greatly increases amplification of the large target. Raw fluorescence values of Lmito ( a ) and Smito ( b ) and hence lesion frequencies ( c ) are affected by digestion. Lesion frequencies represent the decrease in amplification of the large mitochondrial fragment normalized to the small fragment. Data represent the mean+/−SD of two biological samples. Net fluorescence: Picogreen fluorescence of the PCR product minus a “no-template” control

    Techniques Used: Polymerase Chain Reaction, Amplification, Fluorescence

    24) Product Images from "Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins"

    Article Title: Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

    Journal: The Journal of Cell Biology

    doi: 10.1083/jcb.201405110

    H3K9me2/3 is necessary for de novo LAD formation. (A and B) Immunoblot analysis of protein lysates from TCIS lines either harboring Ikzf1 (I) LAS or bound by YY1-EGFP-LacI (−IPTG) and nonswitched control. Cells were treated with either vehicle (DMSO) or 5 µM Bix-01294 for 24 or 60 h. Proteins were detected by the antibodies indicated; loading control is total histone H3. (C) Representative images of clone Y harboring the Ikzf1 (I) LAS ± 5 µM Bix-01294 after 24- or 60-h treatment. EGFP-LacI foci (arrowheads), LMNB1 (red), and Hoechst (blue) are shown. Insets are 300× magnifications. (D) Quantitation of the disposition of the TCIS insert for vehicle and 5 µM Bix-01294 treatment at 24- and 60-h treatment of clone Y harboring Ikzf1 (I) LAS and YY1-EGFP-LacI (−IPTG, n ≥ 50). (E) qPCR analysis of DamID in clone Y harboring Ikzf1 (I) LAS ±5 µM Bix-01294 (60 h). A value > 1, of Dam-LMNB1 over Dam only, indicates enrichment of the tested locus. Positive and negative controls are primers to an internal region of the Igh locus and a non–lamina-associated region, dip, as previously described. The data shown are from a single representative experiment. (F) Quantitation of 3D DNA immuno-FISH for the indicated proteins in 48-h, 5 µM Bix-01294–treated MEFs ( n ≥ 50; *, P ≤ 0.01). (G) Immunoblot analysis of protein lysates from TCIS clone Y harboring Ikzf1 (I) LAS or YY1-EGFP-LacI (−IPTG) treated with the indicated shRNAs. Proteins were detected by the antibodies indicated; loading control is total histone H3. (H) Quantitation of the disposition of TCIS sites of clone Y harboring Ikzf1 (I) LAS or bound by YY1-EGFP-LacI–treated shRNAs as indicated (48 h, n ≥ 50). Error bars indicate SD.
    Figure Legend Snippet: H3K9me2/3 is necessary for de novo LAD formation. (A and B) Immunoblot analysis of protein lysates from TCIS lines either harboring Ikzf1 (I) LAS or bound by YY1-EGFP-LacI (−IPTG) and nonswitched control. Cells were treated with either vehicle (DMSO) or 5 µM Bix-01294 for 24 or 60 h. Proteins were detected by the antibodies indicated; loading control is total histone H3. (C) Representative images of clone Y harboring the Ikzf1 (I) LAS ± 5 µM Bix-01294 after 24- or 60-h treatment. EGFP-LacI foci (arrowheads), LMNB1 (red), and Hoechst (blue) are shown. Insets are 300× magnifications. (D) Quantitation of the disposition of the TCIS insert for vehicle and 5 µM Bix-01294 treatment at 24- and 60-h treatment of clone Y harboring Ikzf1 (I) LAS and YY1-EGFP-LacI (−IPTG, n ≥ 50). (E) qPCR analysis of DamID in clone Y harboring Ikzf1 (I) LAS ±5 µM Bix-01294 (60 h). A value > 1, of Dam-LMNB1 over Dam only, indicates enrichment of the tested locus. Positive and negative controls are primers to an internal region of the Igh locus and a non–lamina-associated region, dip, as previously described. The data shown are from a single representative experiment. (F) Quantitation of 3D DNA immuno-FISH for the indicated proteins in 48-h, 5 µM Bix-01294–treated MEFs ( n ≥ 50; *, P ≤ 0.01). (G) Immunoblot analysis of protein lysates from TCIS clone Y harboring Ikzf1 (I) LAS or YY1-EGFP-LacI (−IPTG) treated with the indicated shRNAs. Proteins were detected by the antibodies indicated; loading control is total histone H3. (H) Quantitation of the disposition of TCIS sites of clone Y harboring Ikzf1 (I) LAS or bound by YY1-EGFP-LacI–treated shRNAs as indicated (48 h, n ≥ 50). Error bars indicate SD.

    Techniques Used: Quantitation Assay, Real-time Polymerase Chain Reaction, Fluorescence In Situ Hybridization

    DZNep treatment leads to loss of peripheral targeting. (A) Immunoblot analysis of H3K27me3 in clones 12 and Y ±5 µM DZNep treatment for 24 h. (B) Representative images of clone Y harboring the Ikzf1 (4) LAS, ±DZNep treatment. EGFP-LacI foci (green, arrowheads) are shown relative to LMNB1 (red) and H3K27me3 (magenta). Insets are 300× magnifications. (C) Quantitation of IF for DZNep treatment of clone Y harboring Igh (N) and Ikzf1 (4) LAS and a nontargeting fragment Ikzf1 (8) ( n ≥ 50; *, P ≤ 0.05). (D) Quantitation of IF of 24-h, 5 µM DZNep-treated clones Y and 12 expressing EGFP-LacI or YY1-EGFP-LacI ( n ≥ 50; *, P ≤ 0.001). Error bars are SD. (E) Quantitation of 3D DNA immuno-FISH for the indicated endogenous loci in MEFs treated with 5 µM DZNep (24 h) MEFs ( n ≥ 50; *, P ≤ 0.05).
    Figure Legend Snippet: DZNep treatment leads to loss of peripheral targeting. (A) Immunoblot analysis of H3K27me3 in clones 12 and Y ±5 µM DZNep treatment for 24 h. (B) Representative images of clone Y harboring the Ikzf1 (4) LAS, ±DZNep treatment. EGFP-LacI foci (green, arrowheads) are shown relative to LMNB1 (red) and H3K27me3 (magenta). Insets are 300× magnifications. (C) Quantitation of IF for DZNep treatment of clone Y harboring Igh (N) and Ikzf1 (4) LAS and a nontargeting fragment Ikzf1 (8) ( n ≥ 50; *, P ≤ 0.05). (D) Quantitation of IF of 24-h, 5 µM DZNep-treated clones Y and 12 expressing EGFP-LacI or YY1-EGFP-LacI ( n ≥ 50; *, P ≤ 0.001). Error bars are SD. (E) Quantitation of 3D DNA immuno-FISH for the indicated endogenous loci in MEFs treated with 5 µM DZNep (24 h) MEFs ( n ≥ 50; *, P ≤ 0.05).

    Techniques Used: Clone Assay, Quantitation Assay, Expressing, Fluorescence In Situ Hybridization

    YY1 targets chromatin to the nuclear periphery. (A) Expression of YY1 and Zbtb7b fusions to EGFP-LacI were verified by immunoblotting by detection with α-GFP. (B) qRT-PCR of Col1A1 and fibronectin in FB cells overexpressing Zbtb7b-EGFP-LacI. (C) Representative images of 3D DNA immuno-FISH. EGFP-LacI, YY1-EGFP-LacI, or Zbtb7b-EGFP-LacI fusion proteins detected by α-LacI (magenta, arrowheads) colocalize with the TCIS insert site ( lacO probe, green, arrowheads) and LMNB1 (red). (D) Quantitation of 3D DNA immuno-FISH for lacO /LacI position in two TCIS clones ( n ≥ 50; *, P ≤ 0.001). Dotted line is the approximate peripheral association of the nonrecombined TCIS insert. (E) qPCR analysis of Dam-LMNB1/Dam in clone Y and 12 under the indicated conditions. A value > 1 for (Dam-LMNB1/Dam only) indicates enrichment. Primers to the TCIS locus, the Igh locus (positive control), and a non–lamina-associated region, dip (negative control), were used for amplification. The data shown are from a single representative experiment. Dotted line is a ratio of 1 for Dam-LaminB/Dam. (F) Representative images of 3D DNA immuno-FISH in clone Y containing either Ikzf1 (I) LAS or YY1-EGFP-LacI (±IPTG). LMNB1 (red), γ-satellite (cyan), lacO probe (green), and Hoechst (blue) are shown. Arrowheads show the disposition of lacO arrays. Insets are 300× magnifications. (G) Quantitation of 3D DNA immuno-FISH for lacO position in relationship to both the nuclear lamina and γ-satellite DNA with either Ikzf1 (I) LAS integrated or YY1 bound ( n ≥ 50; *, P ≤ 0.001). (H) Quantitation of the disposition of lacO sites by 3D immuno-FISH analysis in clone 12 and Y overexpressing YY1-EGFP-LacI (−IPTG) before and after shRNA-mediated knockdown (as indicated; n ≥ 50; *, P ≤ 0.001). Error bars indicate SD.
    Figure Legend Snippet: YY1 targets chromatin to the nuclear periphery. (A) Expression of YY1 and Zbtb7b fusions to EGFP-LacI were verified by immunoblotting by detection with α-GFP. (B) qRT-PCR of Col1A1 and fibronectin in FB cells overexpressing Zbtb7b-EGFP-LacI. (C) Representative images of 3D DNA immuno-FISH. EGFP-LacI, YY1-EGFP-LacI, or Zbtb7b-EGFP-LacI fusion proteins detected by α-LacI (magenta, arrowheads) colocalize with the TCIS insert site ( lacO probe, green, arrowheads) and LMNB1 (red). (D) Quantitation of 3D DNA immuno-FISH for lacO /LacI position in two TCIS clones ( n ≥ 50; *, P ≤ 0.001). Dotted line is the approximate peripheral association of the nonrecombined TCIS insert. (E) qPCR analysis of Dam-LMNB1/Dam in clone Y and 12 under the indicated conditions. A value > 1 for (Dam-LMNB1/Dam only) indicates enrichment. Primers to the TCIS locus, the Igh locus (positive control), and a non–lamina-associated region, dip (negative control), were used for amplification. The data shown are from a single representative experiment. Dotted line is a ratio of 1 for Dam-LaminB/Dam. (F) Representative images of 3D DNA immuno-FISH in clone Y containing either Ikzf1 (I) LAS or YY1-EGFP-LacI (±IPTG). LMNB1 (red), γ-satellite (cyan), lacO probe (green), and Hoechst (blue) are shown. Arrowheads show the disposition of lacO arrays. Insets are 300× magnifications. (G) Quantitation of 3D DNA immuno-FISH for lacO position in relationship to both the nuclear lamina and γ-satellite DNA with either Ikzf1 (I) LAS integrated or YY1 bound ( n ≥ 50; *, P ≤ 0.001). (H) Quantitation of the disposition of lacO sites by 3D immuno-FISH analysis in clone 12 and Y overexpressing YY1-EGFP-LacI (−IPTG) before and after shRNA-mediated knockdown (as indicated; n ≥ 50; *, P ≤ 0.001). Error bars indicate SD.

    Techniques Used: Expressing, Quantitative RT-PCR, Fluorescence In Situ Hybridization, Quantitation Assay, Clone Assay, Real-time Polymerase Chain Reaction, Positive Control, Negative Control, Amplification, shRNA

    Knockdown of Zbtb7b, CTCF, YY1, EZH2, or LMNA/C leads to a loss of peripheral association of LAS. (A) Immunoblot analysis of protein lysates from TCIS lines Y and 12, harboring LAS Ikzf1 (I) (Ik) or Igh (N) and control nonswitched (NS) with either off-target or target shRNA as indicated to the left of each blot. (B and C) Quantitation of IF testing the disposition of lacO and LMNB1 in TCIS clones harboring the Ikzf1 (I) (B) or Igh (N) (C) LAS, after 4-d treatment with the indicated shRNA ( n ≥ 50; *, P ≤ 0.001). (D) Quantitation of 3D DNA immuno-FISH for BAC probes to the indicated endogenous LAD regions in MEFs treated with the indicated shRNA constructs ( n ≥ 50; *, P ≤ 0.05). Error bars indicate SD. Dotted lines are approximate peripheral association of the nonrecombined TCIS insert.
    Figure Legend Snippet: Knockdown of Zbtb7b, CTCF, YY1, EZH2, or LMNA/C leads to a loss of peripheral association of LAS. (A) Immunoblot analysis of protein lysates from TCIS lines Y and 12, harboring LAS Ikzf1 (I) (Ik) or Igh (N) and control nonswitched (NS) with either off-target or target shRNA as indicated to the left of each blot. (B and C) Quantitation of IF testing the disposition of lacO and LMNB1 in TCIS clones harboring the Ikzf1 (I) (B) or Igh (N) (C) LAS, after 4-d treatment with the indicated shRNA ( n ≥ 50; *, P ≤ 0.001). (D) Quantitation of 3D DNA immuno-FISH for BAC probes to the indicated endogenous LAD regions in MEFs treated with the indicated shRNA constructs ( n ≥ 50; *, P ≤ 0.05). Error bars indicate SD. Dotted lines are approximate peripheral association of the nonrecombined TCIS insert.

    Techniques Used: shRNA, Quantitation Assay, Clone Assay, Fluorescence In Situ Hybridization, BAC Assay, Construct

    Both FB and pro–B cell genomes contain vLADs. (A–D) Shown are regions containing the Igh , Ikzf1 , and Bcl11a loci from FB-specific vLADs. (left) Representative images of 3D DNA immuno-FISH of endogenous in FB and pro–B cells. FISH probes detecting the indicated regions are depicted (arrowheads), and the nuclear lamina is demarcated by LMNB1 (red). Quantitation of peripheral association was determined by overlap of FISH probe and LMNB1 ( n ≥ 50). (right) DamID detection of LADs log 2 (Dam-LMNB1/Dam) mean ratios from three experiments for FB (blue) and pro–B cells (orange). Traces above the 0 line indicate a region in a LAD. Solid blue and orange bars underscore LADs in FB and pro–B cells, respectively. Genes are indicated as transcripts (blue), and our gene of interest is red. BAC locations are indicated by green bars, and gray shading indicates an FB-specific vLAD. Chr, chromosome.
    Figure Legend Snippet: Both FB and pro–B cell genomes contain vLADs. (A–D) Shown are regions containing the Igh , Ikzf1 , and Bcl11a loci from FB-specific vLADs. (left) Representative images of 3D DNA immuno-FISH of endogenous in FB and pro–B cells. FISH probes detecting the indicated regions are depicted (arrowheads), and the nuclear lamina is demarcated by LMNB1 (red). Quantitation of peripheral association was determined by overlap of FISH probe and LMNB1 ( n ≥ 50). (right) DamID detection of LADs log 2 (Dam-LMNB1/Dam) mean ratios from three experiments for FB (blue) and pro–B cells (orange). Traces above the 0 line indicate a region in a LAD. Solid blue and orange bars underscore LADs in FB and pro–B cells, respectively. Genes are indicated as transcripts (blue), and our gene of interest is red. BAC locations are indicated by green bars, and gray shading indicates an FB-specific vLAD. Chr, chromosome.

    Techniques Used: Fluorescence In Situ Hybridization, Quantitation Assay, BAC Assay

    25) Product Images from "Evaluation of three DNA extraction methods from fungal cultures"

    Article Title: Evaluation of three DNA extraction methods from fungal cultures

    Journal: Medical Journal, Armed Forces India

    doi: 10.1016/j.mjafi.2017.07.009

    Gel electrophoresis of amplicons generated from DNA extracted by: (Panel 1a and 1b) Fungi/Yeast Genomic DNA Isolation Kit (Norgen). (Panel 2) Qiagen DNA mini kit (QIAamp, Qiagen). (Panel 3) Phenol chloroform iso-amyl alcohol method. C.alb – Candida albicans , C.trop – Candida tropicalis , C.neo – Cryptococcus neoformans ; T.asa – Trichosporon asahii , Pen – Penicillium spp., Fus – Fusarium spp., Epid – Epidermophyton mentagrophytes , M.gyp – Microsporum gypseum , A.fum – Aspergillus fumigatus , Rhizopus – Rhizopus spp., Fusariium – Fusarium spp., M.gyp – Microsporum gypseum , E.mento – Epidermophyton mentagrophytes , Penicillium – Penicillium spp., NC – negative control, MM – 100 bp molecular marker (500 bp is marked).
    Figure Legend Snippet: Gel electrophoresis of amplicons generated from DNA extracted by: (Panel 1a and 1b) Fungi/Yeast Genomic DNA Isolation Kit (Norgen). (Panel 2) Qiagen DNA mini kit (QIAamp, Qiagen). (Panel 3) Phenol chloroform iso-amyl alcohol method. C.alb – Candida albicans , C.trop – Candida tropicalis , C.neo – Cryptococcus neoformans ; T.asa – Trichosporon asahii , Pen – Penicillium spp., Fus – Fusarium spp., Epid – Epidermophyton mentagrophytes , M.gyp – Microsporum gypseum , A.fum – Aspergillus fumigatus , Rhizopus – Rhizopus spp., Fusariium – Fusarium spp., M.gyp – Microsporum gypseum , E.mento – Epidermophyton mentagrophytes , Penicillium – Penicillium spp., NC – negative control, MM – 100 bp molecular marker (500 bp is marked).

    Techniques Used: Nucleic Acid Electrophoresis, Generated, DNA Extraction, Negative Control, Marker

    26) Product Images from "A reliable and rapid method for molecular detection of malarial parasites using microwave irradiation and loop mediated isothermal amplification"

    Article Title: A reliable and rapid method for molecular detection of malarial parasites using microwave irradiation and loop mediated isothermal amplification

    Journal: Malaria Journal

    doi: 10.1186/1475-2875-13-454

    Amplified pfmdr1 gene products after nested PCR. Standard DNA extraction was carried out using the QIAamp DNA mini blood kit (Qiagen, Hilden, Germany). DNA extraction by microwave irradiation was performed using a microwave oven (MDA, model number: MW17M70G-AU, 230 V, 50 HZ, operated at 800 W). 1 μl of condensed droplets after microwave treatment were utilized for the PCR procedures. First lane: DNA ladder; NC: Negative Control; PC1 and PC2: Standard extraction from archived blood sample and pfmdr1 amplicons at expected sizes; PC3 and PC4: Standard extraction from 3D7 P. falciparum parasites in culture and pfmdr1 amplicons at expected sizes; ME1 and ME2: Microwave based extraction from archived blood sample and pfmdr1 amplicons at expected sizes; ME3 and ME4: Microwave based extraction in 3D7 culture parasites and pfmdr1 amplicons at expected sizes; ME5: Microwave based DNA extraction from fresh blood sample and pfmdr1 amplicons at expected sizes.
    Figure Legend Snippet: Amplified pfmdr1 gene products after nested PCR. Standard DNA extraction was carried out using the QIAamp DNA mini blood kit (Qiagen, Hilden, Germany). DNA extraction by microwave irradiation was performed using a microwave oven (MDA, model number: MW17M70G-AU, 230 V, 50 HZ, operated at 800 W). 1 μl of condensed droplets after microwave treatment were utilized for the PCR procedures. First lane: DNA ladder; NC: Negative Control; PC1 and PC2: Standard extraction from archived blood sample and pfmdr1 amplicons at expected sizes; PC3 and PC4: Standard extraction from 3D7 P. falciparum parasites in culture and pfmdr1 amplicons at expected sizes; ME1 and ME2: Microwave based extraction from archived blood sample and pfmdr1 amplicons at expected sizes; ME3 and ME4: Microwave based extraction in 3D7 culture parasites and pfmdr1 amplicons at expected sizes; ME5: Microwave based DNA extraction from fresh blood sample and pfmdr1 amplicons at expected sizes.

    Techniques Used: Amplification, Nested PCR, DNA Extraction, Irradiation, Multiple Displacement Amplification, Polymerase Chain Reaction, Negative Control

    27) Product Images from "DNA demethylation enhances myoblasts hypertrophy during the late phase of myogenesis activating the IGF-I pathway"

    Article Title: DNA demethylation enhances myoblasts hypertrophy during the late phase of myogenesis activating the IGF-I pathway

    Journal: Endocrine

    doi: 10.1007/s12020-013-0142-5

    AZA effects on myoblasts proliferation and on global DNA methylation status. a Growth curve trends were obtain growing myoblasts until 40 % confluence in GM and then were switched in GMAZA or in DM. The experiment continued until the cells reached subconfluence. GMAZA and DM negative influence C2C12 proliferative potential. b Myotoxicity of AZA in vitro: AZA did not induce cell death. c Evaluation of AZA demethylation action on global DNA methylation status. Global DNA methylation levels were evaluated by an ELISA assay specific for 5-mC. d Immunofluorescence MyHC analysis at 48 h in GM, GMAZA, DM, and DMAZA conditions. MyHC positive cells are labeled in red . DAPI and merge images are reported
    Figure Legend Snippet: AZA effects on myoblasts proliferation and on global DNA methylation status. a Growth curve trends were obtain growing myoblasts until 40 % confluence in GM and then were switched in GMAZA or in DM. The experiment continued until the cells reached subconfluence. GMAZA and DM negative influence C2C12 proliferative potential. b Myotoxicity of AZA in vitro: AZA did not induce cell death. c Evaluation of AZA demethylation action on global DNA methylation status. Global DNA methylation levels were evaluated by an ELISA assay specific for 5-mC. d Immunofluorescence MyHC analysis at 48 h in GM, GMAZA, DM, and DMAZA conditions. MyHC positive cells are labeled in red . DAPI and merge images are reported

    Techniques Used: DNA Methylation Assay, In Vitro, Enzyme-linked Immunosorbent Assay, Immunofluorescence, Labeling

    28) Product Images from "Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis"

    Article Title: Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis

    Journal: Clinical chemistry and laboratory medicine : CCLM / FESCC

    doi: 10.1515/cclm-2012-0429

    Electrophoretic analysis of genomic DNA from buccal cell and saliva samples showing mixed results with DNA (100–200 ng) loaded onto 1% agarose gel and visualized using 0.5 μg/mL of ethidium bromide. (A) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from nine infants with developmental delay in which seven DNA samples (Subjects 52, 102, 120, 144, 165, 188, 223) met standardized laboratory criteria for chromosomal microarray analysis based on DNA quantity or yield (e.g., 0.75 μg), purity or qualtiy (i.e., spectrophotometer OD 260/280 ratios; e.g., 1.6–2.1) and sufficient intact high molecular weight DNA using gel electrophoresis. (B) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from three representative infants (Subjects 95, 100, 175) with developmental delay showing the degree of degradation from 10,000 bp to 1000 bp range as designated by known DNA markers and not meeting laboratory criteria whereas a greater yield of high quality intact DNA was found with MasterPure DNA kit in five representative infants (Subjects 106, 112, 117, 122, 135). No intact DNA fragments were visualized below 1000 bp. (C) Chromosomal microarray analysis of buccal DNA from Subject 165 using the Affymetrix Genome-Wide Human SNP Array 6.0 (Santa Clara, CA, USA) to identify genomic deletions or duplications showed a 7 Mb deletion (copy number of 1) of the 20q13.2–20q13.33 region occurring at 53,512,484–60,850,110 bp from the p-terminus of the chromosome. (D) DNA isolated from freshly-collected buccal and saliva using the QIAamp (Qiagen) kit from four control subjects meeting laboratory criteria except for one buccal sample (Subject 2) with a high OD ratio of 2.6 in comparison with DNA isolated from blood and lymphoblasts (L-blast), more conventional sources for DNA, obtained from two different representative control subjects (Subjects 1046, 1047) showing the typical DNA pattern with gel electrophoresis ranging from 10,000 bp to 1000 bp designated by known DNA markers. No intact DNA fragments were visualized below 1000 bp.
    Figure Legend Snippet: Electrophoretic analysis of genomic DNA from buccal cell and saliva samples showing mixed results with DNA (100–200 ng) loaded onto 1% agarose gel and visualized using 0.5 μg/mL of ethidium bromide. (A) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from nine infants with developmental delay in which seven DNA samples (Subjects 52, 102, 120, 144, 165, 188, 223) met standardized laboratory criteria for chromosomal microarray analysis based on DNA quantity or yield (e.g., 0.75 μg), purity or qualtiy (i.e., spectrophotometer OD 260/280 ratios; e.g., 1.6–2.1) and sufficient intact high molecular weight DNA using gel electrophoresis. (B) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from three representative infants (Subjects 95, 100, 175) with developmental delay showing the degree of degradation from 10,000 bp to 1000 bp range as designated by known DNA markers and not meeting laboratory criteria whereas a greater yield of high quality intact DNA was found with MasterPure DNA kit in five representative infants (Subjects 106, 112, 117, 122, 135). No intact DNA fragments were visualized below 1000 bp. (C) Chromosomal microarray analysis of buccal DNA from Subject 165 using the Affymetrix Genome-Wide Human SNP Array 6.0 (Santa Clara, CA, USA) to identify genomic deletions or duplications showed a 7 Mb deletion (copy number of 1) of the 20q13.2–20q13.33 region occurring at 53,512,484–60,850,110 bp from the p-terminus of the chromosome. (D) DNA isolated from freshly-collected buccal and saliva using the QIAamp (Qiagen) kit from four control subjects meeting laboratory criteria except for one buccal sample (Subject 2) with a high OD ratio of 2.6 in comparison with DNA isolated from blood and lymphoblasts (L-blast), more conventional sources for DNA, obtained from two different representative control subjects (Subjects 1046, 1047) showing the typical DNA pattern with gel electrophoresis ranging from 10,000 bp to 1000 bp designated by known DNA markers. No intact DNA fragments were visualized below 1000 bp.

    Techniques Used: Agarose Gel Electrophoresis, Isolation, Microarray, Spectrophotometry, Molecular Weight, Nucleic Acid Electrophoresis, Genome Wide

    29) Product Images from "The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer"

    Article Title: The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer

    Journal: Cell Death & Disease

    doi: 10.1038/s41419-017-0137-x

    DNMT1 maintains CHFR gene expression via promoter DNA methylation, and CHFR participates in UBC13 regulating paclitaxel sensitivity a Detection of methylation status at the promoter region of the CHFR gene in A2780, SKOV3, and 3AO cells with DNMT1-knockdown by Bisulfite sequencing. Ten lines with circles represent the same sequence of ten clones from one sample. CpG sites are shown as filled circles (methylated) or unfilled circles (unmethylated). The lower panel shows the summary data. * P
    Figure Legend Snippet: DNMT1 maintains CHFR gene expression via promoter DNA methylation, and CHFR participates in UBC13 regulating paclitaxel sensitivity a Detection of methylation status at the promoter region of the CHFR gene in A2780, SKOV3, and 3AO cells with DNMT1-knockdown by Bisulfite sequencing. Ten lines with circles represent the same sequence of ten clones from one sample. CpG sites are shown as filled circles (methylated) or unfilled circles (unmethylated). The lower panel shows the summary data. * P

    Techniques Used: Expressing, DNA Methylation Assay, Methylation, Methylation Sequencing, Sequencing, Clone Assay

    Paclitaxel exposure reduces UBC13 and CHFR, increases DNMT1 and Aurora A Western blotting of the indicated proteins in a A2780 and b SKOV3 cells treated with 2, 5, and 10 nM paclitaxel for the indicated times. Cells without paclitaxel treatment were assigned to be the blank control (0 h). One of three representative results is shown. c Working model: UBC13 regulates paclitaxel resistance via DNMT1/CHFR/Aurora A in ovarian cancer cells. UBC13 reduces DNMT1 through ubiquitination, results in DNA hypomethylation of the CHFR promoter, and decreases Aurora A. Reduction of UBC13 increases stability of DNMT1, leads to hypermethylation of the CHFR promoter, elevates Aurora A levels, and prompts paclitaxel resistance in ovarian cancer cells. Ub: ubiquitin
    Figure Legend Snippet: Paclitaxel exposure reduces UBC13 and CHFR, increases DNMT1 and Aurora A Western blotting of the indicated proteins in a A2780 and b SKOV3 cells treated with 2, 5, and 10 nM paclitaxel for the indicated times. Cells without paclitaxel treatment were assigned to be the blank control (0 h). One of three representative results is shown. c Working model: UBC13 regulates paclitaxel resistance via DNMT1/CHFR/Aurora A in ovarian cancer cells. UBC13 reduces DNMT1 through ubiquitination, results in DNA hypomethylation of the CHFR promoter, and decreases Aurora A. Reduction of UBC13 increases stability of DNMT1, leads to hypermethylation of the CHFR promoter, elevates Aurora A levels, and prompts paclitaxel resistance in ovarian cancer cells. Ub: ubiquitin

    Techniques Used: Western Blot

    Differential expressions of proteins between paclitaxel sensitive and resistant ovarian cancer cells by proteomic analysis a Analysis of SKOV3 and SKOV3-TR30 samples by DIGE. Fluorescent (left) and monochrome (right) images of the DIGE Gel. Proteins extracted from SKOV3 (SK) and SKOV3-TR30 (ST) were labeled with Cy3 and Cy5, respectively. The labeled samples were initially separated in the first dimension ( x -axis) on a non-linear gradient pH 3-10, then separated in the second dimension ( y -axis) on a 12% polyacrylamide gel. The circled spots were identified by MALDI-TOF/TOF MS/MS analysis shown in the supplementary material Table S1 – S3 . b Three-dimensional volumetric models of UBC13 in SKOV3 (top) and SKOV3-TR30 (bottom) for DIGE spots. c The expression levels of UBC13 shown on DIGE were calculated by DeCyder analysis and presented as standardized log abundance. SK presents SKOV3 and ST presents SKOV3-TR30. d Western blotting of UBC13 in A2780 vs. A2780-TR and SKOV3 vs. SKOV3-TR30 cells, respectively. One of three representative results is shown in ( d )
    Figure Legend Snippet: Differential expressions of proteins between paclitaxel sensitive and resistant ovarian cancer cells by proteomic analysis a Analysis of SKOV3 and SKOV3-TR30 samples by DIGE. Fluorescent (left) and monochrome (right) images of the DIGE Gel. Proteins extracted from SKOV3 (SK) and SKOV3-TR30 (ST) were labeled with Cy3 and Cy5, respectively. The labeled samples were initially separated in the first dimension ( x -axis) on a non-linear gradient pH 3-10, then separated in the second dimension ( y -axis) on a 12% polyacrylamide gel. The circled spots were identified by MALDI-TOF/TOF MS/MS analysis shown in the supplementary material Table S1 – S3 . b Three-dimensional volumetric models of UBC13 in SKOV3 (top) and SKOV3-TR30 (bottom) for DIGE spots. c The expression levels of UBC13 shown on DIGE were calculated by DeCyder analysis and presented as standardized log abundance. SK presents SKOV3 and ST presents SKOV3-TR30. d Western blotting of UBC13 in A2780 vs. A2780-TR and SKOV3 vs. SKOV3-TR30 cells, respectively. One of three representative results is shown in ( d )

    Techniques Used: Labeling, Mass Spectrometry, Expressing, Western Blot

    UBC13 controls DNMT1 stability via ubiquitination and DNMT1 participates in UBC13 regulation of the paclitaxel sensitivity DNMT1 ubiquitination in a A2780 and b SKOV3 cells with UBC13-overexpression or c A2780 and d SKOV3 with UBC13-knockdown without or with HA-ubiquitin. Cells were treated with MG-132 (20 μM, 8 h) prior to preparation of lysates and then subjected to IP followed by western blot with the indicated antibodies. e Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days, and treated with paclitaxel at the indicated concentrations. f Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days. g Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were treated with paclitaxel at the indicated concentrations. h Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown. Results are shown as means ± SEM for at least three separate experiments in ( e and g ) (* P
    Figure Legend Snippet: UBC13 controls DNMT1 stability via ubiquitination and DNMT1 participates in UBC13 regulation of the paclitaxel sensitivity DNMT1 ubiquitination in a A2780 and b SKOV3 cells with UBC13-overexpression or c A2780 and d SKOV3 with UBC13-knockdown without or with HA-ubiquitin. Cells were treated with MG-132 (20 μM, 8 h) prior to preparation of lysates and then subjected to IP followed by western blot with the indicated antibodies. e Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days, and treated with paclitaxel at the indicated concentrations. f Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown, which were transfected in advance with UBC13-specific shRNA and selected with G418 (400 μg/mL) for 14 days. g Cell viability assays in A2780 and SKOV3 cells with DNMT1-knockdown, which were treated with paclitaxel at the indicated concentrations. h Western blotting of UBC13, DNMT1, CHFR, and Aurora A in A2780 and SKOV3 cells with DNMT1-knockdown. Results are shown as means ± SEM for at least three separate experiments in ( e and g ) (* P

    Techniques Used: Over Expression, Western Blot, Transfection, shRNA

    Paclitaxel induces UBC13 down-regulation, and UBC13 modulates the paclitaxel sensitivity through the DNMT1, CHFR, and Aurora A pathway a A2780 and b SKOV3 cells were treated with 5, 10, 20, and 30 nM paclitaxel for 24 h. Western blotting was performed with the indicated antibodies. Cell viability assays in A2780 and SKOV3 cells with c UBC13-knockdown and d UBC13-overexpression that were treated with paclitaxel at the indicated concentrations. Results are shown as means ± SEM for at least three separate experiments (* P
    Figure Legend Snippet: Paclitaxel induces UBC13 down-regulation, and UBC13 modulates the paclitaxel sensitivity through the DNMT1, CHFR, and Aurora A pathway a A2780 and b SKOV3 cells were treated with 5, 10, 20, and 30 nM paclitaxel for 24 h. Western blotting was performed with the indicated antibodies. Cell viability assays in A2780 and SKOV3 cells with c UBC13-knockdown and d UBC13-overexpression that were treated with paclitaxel at the indicated concentrations. Results are shown as means ± SEM for at least three separate experiments (* P

    Techniques Used: Western Blot, Over Expression

    30) Product Images from "Survivin as a potential therapeutic target of acetylsalicylic acid in pituitary adenomas"

    Article Title: Survivin as a potential therapeutic target of acetylsalicylic acid in pituitary adenomas

    Journal: Oncotarget

    doi: 10.18632/oncotarget.25650

    Effect of ASA treatment on pituitary adenoma cells (A)  Cell proliferation in RC-4 B/C cells but not GH3 cells decreased after 2.5 and 5 mM ASA treatment  (B)  Cell cycle analysis using flow cytometry in RC-4 B/C cells showed decrease in S phase and increase in G2/M phase population upon ASA treatment.  (C)  Survivin mRNA and protein expression decreased after ASA treatment.  * : p=0.013;  **** : p
    Figure Legend Snippet: Effect of ASA treatment on pituitary adenoma cells (A) Cell proliferation in RC-4 B/C cells but not GH3 cells decreased after 2.5 and 5 mM ASA treatment (B) Cell cycle analysis using flow cytometry in RC-4 B/C cells showed decrease in S phase and increase in G2/M phase population upon ASA treatment. (C) Survivin mRNA and protein expression decreased after ASA treatment. * : p=0.013; **** : p

    Techniques Used: Cell Cycle Assay, Flow Cytometry, Cytometry, Expressing

    Effect of survivin inhibition (A)  Survivin silencing by siRNA on RC-4 B/C cells.  (B)  Survivin inhibition by YM155, a small molecule inhibitor in RC-4 B/C cells. The effect of YM155  (C)  and survivin siRNA  (D)  on pituitary adenoma cell viability, proliferation and cell cycle phases of RC-4 B/C cells (see details in the text).  (E)  Decrease of CCNA2, CDK2 mRNA and CCNA2, total CDK2 and p-CDK2 protein abundance following ASA treatment in RC-4 B/C cells.  Left:  mRNA,  middle  and  right : western blot and densitometry.  (F)  YM155 and survivin siRNA transfection did not significantly alter CCNA2 and CDK2 expression in RC-4 B/C cells.  (G)  Survivin overexpression did not reduce the viability of RC-4 B/C cells.  * : p
    Figure Legend Snippet: Effect of survivin inhibition (A) Survivin silencing by siRNA on RC-4 B/C cells. (B) Survivin inhibition by YM155, a small molecule inhibitor in RC-4 B/C cells. The effect of YM155 (C) and survivin siRNA (D) on pituitary adenoma cell viability, proliferation and cell cycle phases of RC-4 B/C cells (see details in the text). (E) Decrease of CCNA2, CDK2 mRNA and CCNA2, total CDK2 and p-CDK2 protein abundance following ASA treatment in RC-4 B/C cells. Left: mRNA, middle and right : western blot and densitometry. (F) YM155 and survivin siRNA transfection did not significantly alter CCNA2 and CDK2 expression in RC-4 B/C cells. (G) Survivin overexpression did not reduce the viability of RC-4 B/C cells. * : p

    Techniques Used: Inhibition, Western Blot, Transfection, Expressing, Over Expression

    31) Product Images from "An LSC epigenetic signature is largely mutation independent and implicates the HOXA cluster in AML pathogenesis"

    Article Title: An LSC epigenetic signature is largely mutation independent and implicates the HOXA cluster in AML pathogenesis

    Journal: Nature Communications

    doi: 10.1038/ncomms9489

    The LSC epigenetic signature is associated with overall survival in human AML. ( a ) TCGA samples were classified as LSC like or Blast like based on DNA methylation alone by generating methylation profiles of the LSC and Blast populations, and then calculating scores of each sample based on the probability of being closer to either LSC or Blast. Kaplan–Meier survival analysis was then applied to these groups as indicated. Statistical significance was determined by the log-rank test ( n =192; 93 LSC-like and 99 Blast-like patients). ( b – e ) Expression of the LSC epigenetic signature genes was combined to create an LSC score, which was then calculated in AML samples. The first principal component of genes in the LSC signature was computed, and patients were stratified as ‘high' or ‘low' relative to its median value in four independent cohorts including TCGA ( n =182; 91 high-score and 91 low-score patients), ( b ) Metzeler et al . ( n =163; 81 high-score and 82 low-score patients) ( c ), Wouters et al . ( n =262; 131 high-score and 131 low-score patients) ( d ) and Wilson et al . ( n =169, 84 high-score and 85 low-score patients) ( e ). In each cohort, patients were classified into high and low groups based on the median value. Kaplan–Meier survival analysis was then applied to these groups as indicated. Statistical significance was determined by the log-rank test.
    Figure Legend Snippet: The LSC epigenetic signature is associated with overall survival in human AML. ( a ) TCGA samples were classified as LSC like or Blast like based on DNA methylation alone by generating methylation profiles of the LSC and Blast populations, and then calculating scores of each sample based on the probability of being closer to either LSC or Blast. Kaplan–Meier survival analysis was then applied to these groups as indicated. Statistical significance was determined by the log-rank test ( n =192; 93 LSC-like and 99 Blast-like patients). ( b – e ) Expression of the LSC epigenetic signature genes was combined to create an LSC score, which was then calculated in AML samples. The first principal component of genes in the LSC signature was computed, and patients were stratified as ‘high' or ‘low' relative to its median value in four independent cohorts including TCGA ( n =182; 91 high-score and 91 low-score patients), ( b ) Metzeler et al . ( n =163; 81 high-score and 82 low-score patients) ( c ), Wouters et al . ( n =262; 131 high-score and 131 low-score patients) ( d ) and Wilson et al . ( n =169, 84 high-score and 85 low-score patients) ( e ). In each cohort, patients were classified into high and low groups based on the median value. Kaplan–Meier survival analysis was then applied to these groups as indicated. Statistical significance was determined by the log-rank test.

    Techniques Used: DNA Methylation Assay, Methylation, Expressing

    Epigenetic signatures define subgroups of AML LSC reflecting the cell of origin. ( a ) A total of 216 DMRs identified from all possible pairwise comparisons among six HSPCs were used to cluster all normal HSPCs with all AML subpopulations. The primary AML subpopulations form two major clusters: L-MPP like and GMP like. LSC subpopulations are indicated in bold. ( b ) Clustering analysis of TCGA AML samples with normal human HSPC using the 216 DMRs shows that the L-MPP-like and GMP-like clusters are observed in this cohort as well. ( c ) TCGA samples were classified according to normal HSPC populations based on DNA methylation alone by generating methylation profiles of all the normal HSPC, and then calculating scores of each sample based on the closest population. The normal progenitor cell identity for all the TCGA samples is indicated. ( d ) The L-MPP-like and GMP-like TCGA samples were grouped according to their FAB classification. NA, not classified.
    Figure Legend Snippet: Epigenetic signatures define subgroups of AML LSC reflecting the cell of origin. ( a ) A total of 216 DMRs identified from all possible pairwise comparisons among six HSPCs were used to cluster all normal HSPCs with all AML subpopulations. The primary AML subpopulations form two major clusters: L-MPP like and GMP like. LSC subpopulations are indicated in bold. ( b ) Clustering analysis of TCGA AML samples with normal human HSPC using the 216 DMRs shows that the L-MPP-like and GMP-like clusters are observed in this cohort as well. ( c ) TCGA samples were classified according to normal HSPC populations based on DNA methylation alone by generating methylation profiles of all the normal HSPC, and then calculating scores of each sample based on the closest population. The normal progenitor cell identity for all the TCGA samples is indicated. ( d ) The L-MPP-like and GMP-like TCGA samples were grouped according to their FAB classification. NA, not classified.

    Techniques Used: DNA Methylation Assay, Methylation

    32) Product Images from "Distinct MicroRNA Expression Signatures of Porcine Induced Pluripotent Stem Cells under Mouse and Human ESC Culture Conditions"

    Article Title: Distinct MicroRNA Expression Signatures of Porcine Induced Pluripotent Stem Cells under Mouse and Human ESC Culture Conditions

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0158655

    The piPSCs-enriched miRNA cluster promotes the reprogramming of porcine cells. (A) The DIANA miPath program predict the pathways regulated by the miR-106a-363 cluster. Heatmap of the miR-106a-363 cluster versus other pathways, where the miRNAs are clustered together when they exhibited similar pathway-targeting patterns, and the pathways are clustered together by related miRNAs. (B) The DIANA miPath program predicted the pathways regulated by the miR-302 cluster. (C) The PCR region used to clone the genomic locus of the miR-106a-363 cluster and putative miR-302 cluster. (D) Amplification of the genomic region containing the miR-106a-363 cluster and putative miRNA-302 cluster. An approximately 1.5 kb range harboring the whole miRNA-106a-363 cluster and a 2 kb range containing the putative porcine miR-302 cluster were amplified. The marker indicates the DNA ladder. (E) AP staining of the piPSCs colonies. (F) Statistical analysis of AP positive colonies. Mean values ± SD are shown. ***P-value
    Figure Legend Snippet: The piPSCs-enriched miRNA cluster promotes the reprogramming of porcine cells. (A) The DIANA miPath program predict the pathways regulated by the miR-106a-363 cluster. Heatmap of the miR-106a-363 cluster versus other pathways, where the miRNAs are clustered together when they exhibited similar pathway-targeting patterns, and the pathways are clustered together by related miRNAs. (B) The DIANA miPath program predicted the pathways regulated by the miR-302 cluster. (C) The PCR region used to clone the genomic locus of the miR-106a-363 cluster and putative miR-302 cluster. (D) Amplification of the genomic region containing the miR-106a-363 cluster and putative miRNA-302 cluster. An approximately 1.5 kb range harboring the whole miRNA-106a-363 cluster and a 2 kb range containing the putative porcine miR-302 cluster were amplified. The marker indicates the DNA ladder. (E) AP staining of the piPSCs colonies. (F) Statistical analysis of AP positive colonies. Mean values ± SD are shown. ***P-value

    Techniques Used: Polymerase Chain Reaction, Amplification, Marker, Staining

    33) Product Images from "DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis"

    Article Title: DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis

    Journal: Biopreservation and Biobanking

    doi: 10.1089/bio.2015.0064

    DNA integrity observation by electrophoresis in agarose gel. DNA samples were analyzed by loading 50 ng of DNA on a 0.8% agarose gel. The Lambda-pUC Mix Marker 4 (MW) was also separated as size reference. Four representative samples of DNA for frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) are shown.
    Figure Legend Snippet: DNA integrity observation by electrophoresis in agarose gel. DNA samples were analyzed by loading 50 ng of DNA on a 0.8% agarose gel. The Lambda-pUC Mix Marker 4 (MW) was also separated as size reference. Four representative samples of DNA for frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) are shown.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Marker, Formalin-fixed Paraffin-Embedded

    DNA purity 260/230 ratio. Absorbance at 260 and 230 nm was measured for each DNA sample isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C), and saliva (D) , and 260/230 ratio obtained was represented versus its corresponding DNA concentration based on spectrophotometric measurement. The trendline for each group of samples is shown. FFPE, formalin-fixed paraffin-embedded; OCT, optimal cutting temperature.
    Figure Legend Snippet: DNA purity 260/230 ratio. Absorbance at 260 and 230 nm was measured for each DNA sample isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C), and saliva (D) , and 260/230 ratio obtained was represented versus its corresponding DNA concentration based on spectrophotometric measurement. The trendline for each group of samples is shown. FFPE, formalin-fixed paraffin-embedded; OCT, optimal cutting temperature.

    Techniques Used: Isolation, Formalin-fixed Paraffin-Embedded, Concentration Assay

    DNA performance for real-time PCR assay. Fifteen randomized DNA samples isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) were amplified by real-time PCR for the GAPDH ( left ) and RPLP0 ( right ) genes. The average C T value and standard deviation for each type of source were calculated. PCR, polymerase chain reaction.
    Figure Legend Snippet: DNA performance for real-time PCR assay. Fifteen randomized DNA samples isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) were amplified by real-time PCR for the GAPDH ( left ) and RPLP0 ( right ) genes. The average C T value and standard deviation for each type of source were calculated. PCR, polymerase chain reaction.

    Techniques Used: Real-time Polymerase Chain Reaction, Isolation, Formalin-fixed Paraffin-Embedded, Amplification, Standard Deviation, Polymerase Chain Reaction

    PicoGreen ® /A260 yield ratio. PicoGreen DNA quantification and DNA quantification using Lambert–Beer law from 260 nm absorbance were performed for each DNA sample isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) . Absolute yields in micrograms of DNA obtained for both methods were calculated. The average ratio and standard deviation of the ratio between absolute yield using PicoGreen and spectrophotometry for each type of source are represented.
    Figure Legend Snippet: PicoGreen ® /A260 yield ratio. PicoGreen DNA quantification and DNA quantification using Lambert–Beer law from 260 nm absorbance were performed for each DNA sample isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) . Absolute yields in micrograms of DNA obtained for both methods were calculated. The average ratio and standard deviation of the ratio between absolute yield using PicoGreen and spectrophotometry for each type of source are represented.

    Techniques Used: Isolation, Formalin-fixed Paraffin-Embedded, Standard Deviation, Spectrophotometry

    DNA quality for PCR analysis. Fifteen randomized DNA samples isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) were amplified by PCR for the ACVR2B , ZFX , AF4 , and GAPDH genes. PCR products of 5049, 1137, 400, and 87 bp, respectively, were analyzed by agarose gel electrophoresis. Four representative samples for each group are shown.
    Figure Legend Snippet: DNA quality for PCR analysis. Fifteen randomized DNA samples isolated from frozen tissue in OCT (A) , FFPE tissue (B) , frozen blood (C) , and saliva (D) were amplified by PCR for the ACVR2B , ZFX , AF4 , and GAPDH genes. PCR products of 5049, 1137, 400, and 87 bp, respectively, were analyzed by agarose gel electrophoresis. Four representative samples for each group are shown.

    Techniques Used: Polymerase Chain Reaction, Isolation, Formalin-fixed Paraffin-Embedded, Amplification, Agarose Gel Electrophoresis

    34) Product Images from "Epigenetic Methylation of Parathyroid CaR and VDR Promoters in Experimental Secondary Hyperparathyroidism"

    Article Title: Epigenetic Methylation of Parathyroid CaR and VDR Promoters in Experimental Secondary Hyperparathyroidism

    Journal: International Journal of Nephrology

    doi: 10.1155/2012/123576

    Methylation detection of CaR and VDR promoter regions in parathyroid glands. Analysis of the CaR and VDR promoter regions by PCR melting curve analysis after bisulfite treatment of genomic DNA. CaR is covered by PCR products CaR #1-2, and VDR is covered by PCR products VDR #1–4. Commercial low- and high-methylated rat DNA is analyzed in all of the PCR reactions shown in the “Methylation control” panel in green and red, respectively; it is also included in the “Sham,” “Uremia,” and “ in vitro ” panels. Control of methylation detection verified high levels of methylation in H19 and VDR downstream gene regions.
    Figure Legend Snippet: Methylation detection of CaR and VDR promoter regions in parathyroid glands. Analysis of the CaR and VDR promoter regions by PCR melting curve analysis after bisulfite treatment of genomic DNA. CaR is covered by PCR products CaR #1-2, and VDR is covered by PCR products VDR #1–4. Commercial low- and high-methylated rat DNA is analyzed in all of the PCR reactions shown in the “Methylation control” panel in green and red, respectively; it is also included in the “Sham,” “Uremia,” and “ in vitro ” panels. Control of methylation detection verified high levels of methylation in H19 and VDR downstream gene regions.

    Techniques Used: Methylation, Polymerase Chain Reaction, In Vitro

    35) Product Images from "Development, validation and evaluation of a rapid PCR-nucleic acid lateral flow immuno-assay for the detection of Plasmodium and the differentiation between Plasmodium falciparum and Plasmodium vivax"

    Article Title: Development, validation and evaluation of a rapid PCR-nucleic acid lateral flow immuno-assay for the detection of Plasmodium and the differentiation between Plasmodium falciparum and Plasmodium vivax

    Journal: Malaria Journal

    doi: 10.1186/1475-2875-11-279

    Examples of the different test outcomes of the PCR-NALFIA. a ) No control and no test line are visible. This is a test failure but can also be seen when only water is amplified (negative control) b ) A positive control line and a negative test line are visible indicating that the test is valid but that no parasite DNA is detected c ) Next to the control a Plasmodium line and a specific line for P. falciparum is present indicating a P. falciparum infection d ) Next to the control and Plasmodium line the specific line for P. vivax is visible indicating a P. vivax infection. e ) Both a positive control and a positive test line for Plasmodium are visible indicating a valid test positive for Plasmodium but negative for P. falciparum and P. vivax .
    Figure Legend Snippet: Examples of the different test outcomes of the PCR-NALFIA. a ) No control and no test line are visible. This is a test failure but can also be seen when only water is amplified (negative control) b ) A positive control line and a negative test line are visible indicating that the test is valid but that no parasite DNA is detected c ) Next to the control a Plasmodium line and a specific line for P. falciparum is present indicating a P. falciparum infection d ) Next to the control and Plasmodium line the specific line for P. vivax is visible indicating a P. vivax infection. e ) Both a positive control and a positive test line for Plasmodium are visible indicating a valid test positive for Plasmodium but negative for P. falciparum and P. vivax .

    Techniques Used: Polymerase Chain Reaction, Amplification, Negative Control, Positive Control, Infection

    36) Product Images from "Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis"

    Article Title: Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis

    Journal: Clinical chemistry and laboratory medicine : CCLM / FESCC

    doi: 10.1515/cclm-2012-0429

    Electrophoretic analysis of genomic DNA from buccal cell and saliva samples showing mixed results with DNA (100–200 ng) loaded onto 1% agarose gel and visualized using 0.5 μg/mL of ethidium bromide. (A) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from nine infants with developmental delay in which seven DNA samples (Subjects 52, 102, 120, 144, 165, 188, 223) met standardized laboratory criteria for chromosomal microarray analysis based on DNA quantity or yield (e.g., 0.75 μg), purity or qualtiy (i.e., spectrophotometer OD 260/280 ratios; e.g., 1.6–2.1) and sufficient intact high molecular weight DNA using gel electrophoresis. (B) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from three representative infants (Subjects 95, 100, 175) with developmental delay showing the degree of degradation from 10,000 bp to 1000 bp range as designated by known DNA markers and not meeting laboratory criteria whereas a greater yield of high quality intact DNA was found with MasterPure DNA kit in five representative infants (Subjects 106, 112, 117, 122, 135). No intact DNA fragments were visualized below 1000 bp. (C) Chromosomal microarray analysis of buccal DNA from Subject 165 using the Affymetrix Genome-Wide Human SNP Array 6.0 (Santa Clara, CA, USA) to identify genomic deletions or duplications showed a 7 Mb deletion (copy number of 1) of the 20q13.2–20q13.33 region occurring at 53,512,484–60,850,110 bp from the p-terminus of the chromosome. (D) DNA isolated from freshly-collected buccal and saliva using the QIAamp (Qiagen) kit from four control subjects meeting laboratory criteria except for one buccal sample (Subject 2) with a high OD ratio of 2.6 in comparison with DNA isolated from blood and lymphoblasts (L-blast), more conventional sources for DNA, obtained from two different representative control subjects (Subjects 1046, 1047) showing the typical DNA pattern with gel electrophoresis ranging from 10,000 bp to 1000 bp designated by known DNA markers. No intact DNA fragments were visualized below 1000 bp.
    Figure Legend Snippet: Electrophoretic analysis of genomic DNA from buccal cell and saliva samples showing mixed results with DNA (100–200 ng) loaded onto 1% agarose gel and visualized using 0.5 μg/mL of ethidium bromide. (A) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from nine infants with developmental delay in which seven DNA samples (Subjects 52, 102, 120, 144, 165, 188, 223) met standardized laboratory criteria for chromosomal microarray analysis based on DNA quantity or yield (e.g., 0.75 μg), purity or qualtiy (i.e., spectrophotometer OD 260/280 ratios; e.g., 1.6–2.1) and sufficient intact high molecular weight DNA using gel electrophoresis. (B) Stored buccal cell DNA isolated with the QIAamp (Qiagen) kit from three representative infants (Subjects 95, 100, 175) with developmental delay showing the degree of degradation from 10,000 bp to 1000 bp range as designated by known DNA markers and not meeting laboratory criteria whereas a greater yield of high quality intact DNA was found with MasterPure DNA kit in five representative infants (Subjects 106, 112, 117, 122, 135). No intact DNA fragments were visualized below 1000 bp. (C) Chromosomal microarray analysis of buccal DNA from Subject 165 using the Affymetrix Genome-Wide Human SNP Array 6.0 (Santa Clara, CA, USA) to identify genomic deletions or duplications showed a 7 Mb deletion (copy number of 1) of the 20q13.2–20q13.33 region occurring at 53,512,484–60,850,110 bp from the p-terminus of the chromosome. (D) DNA isolated from freshly-collected buccal and saliva using the QIAamp (Qiagen) kit from four control subjects meeting laboratory criteria except for one buccal sample (Subject 2) with a high OD ratio of 2.6 in comparison with DNA isolated from blood and lymphoblasts (L-blast), more conventional sources for DNA, obtained from two different representative control subjects (Subjects 1046, 1047) showing the typical DNA pattern with gel electrophoresis ranging from 10,000 bp to 1000 bp designated by known DNA markers. No intact DNA fragments were visualized below 1000 bp.

    Techniques Used: Agarose Gel Electrophoresis, Isolation, Microarray, Spectrophotometry, Molecular Weight, Nucleic Acid Electrophoresis, Genome Wide

    37) Product Images from "Epidemiological and molecular investigation of resurgent cutaneous leishmaniasis in Sudan"

    Article Title: Epidemiological and molecular investigation of resurgent cutaneous leishmaniasis in Sudan

    Journal: International Journal of Infectious Diseases

    doi: 10.1016/j.ijid.2019.08.018

    PCR-RFLP identification of Leishmania species from cutaneous leishmaniasis lesions. (A) DNA extracted from ATL buffer, CL05 and CL06 produced the RFLP pattern characteristic of Leishmania major , with band sizes as described in the text. (B) DNA extracted from culture of the isolate from CL08 (MHOM/SD/2017/ELOBIED) also gave the pattern typical of L. major ; PCR-RFLP of L. tropica was included as control. The L. major identification was verified by DNA sequencing (see text).
    Figure Legend Snippet: PCR-RFLP identification of Leishmania species from cutaneous leishmaniasis lesions. (A) DNA extracted from ATL buffer, CL05 and CL06 produced the RFLP pattern characteristic of Leishmania major , with band sizes as described in the text. (B) DNA extracted from culture of the isolate from CL08 (MHOM/SD/2017/ELOBIED) also gave the pattern typical of L. major ; PCR-RFLP of L. tropica was included as control. The L. major identification was verified by DNA sequencing (see text).

    Techniques Used: Polymerase Chain Reaction, Produced, DNA Sequencing

    38) Product Images from "High-density array analysis of DNA methylation in Tamoxifen-resistant breast cancer cell lines"

    Article Title: High-density array analysis of DNA methylation in Tamoxifen-resistant breast cancer cell lines

    Journal: Epigenetics

    doi: 10.4161/epi.27111

    Figure 2. Scatter plots indicate genome-wide methylation changes in Tamoxifen-resistant lines compared with the parental. TMX2–11 ( A ), TMX2–28 ( B ) and MCF-7 treated with 10 −10 M E 2 for 14 d ( D ) were compared with the parental
    Figure Legend Snippet: Figure 2. Scatter plots indicate genome-wide methylation changes in Tamoxifen-resistant lines compared with the parental. TMX2–11 ( A ), TMX2–28 ( B ) and MCF-7 treated with 10 −10 M E 2 for 14 d ( D ) were compared with the parental

    Techniques Used: Genome Wide, Methylation

    Figure 3. Location of aberrantly methylated CpG sites shared between TMX2–11 and TMX2–28. Functional genomic location of all CpG sites on the BeadChip ( A ) hypermethylated ( B ) and hypomethylated ( C ) CpG sites. Neighborhood location
    Figure Legend Snippet: Figure 3. Location of aberrantly methylated CpG sites shared between TMX2–11 and TMX2–28. Functional genomic location of all CpG sites on the BeadChip ( A ) hypermethylated ( B ) and hypomethylated ( C ) CpG sites. Neighborhood location

    Techniques Used: Methylation, Functional Assay

    39) Product Images from "The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer"

    Article Title: The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer

    Journal: Cell Death & Disease

    doi: 10.1038/s41419-017-0137-x

    DNMT1 maintains CHFR gene expression via promoter DNA methylation, and CHFR participates in UBC13 regulating paclitaxel sensitivity a Detection of methylation status at the promoter region of the CHFR gene in A2780, SKOV3, and 3AO cells with DNMT1-knockdown by Bisulfite sequencing. Ten lines with circles represent the same sequence of ten clones from one sample. CpG sites are shown as filled circles (methylated) or unfilled circles (unmethylated). The lower panel shows the summary data. * P
    Figure Legend Snippet: DNMT1 maintains CHFR gene expression via promoter DNA methylation, and CHFR participates in UBC13 regulating paclitaxel sensitivity a Detection of methylation status at the promoter region of the CHFR gene in A2780, SKOV3, and 3AO cells with DNMT1-knockdown by Bisulfite sequencing. Ten lines with circles represent the same sequence of ten clones from one sample. CpG sites are shown as filled circles (methylated) or unfilled circles (unmethylated). The lower panel shows the summary data. * P

    Techniques Used: Expressing, DNA Methylation Assay, Methylation, Methylation Sequencing, Sequencing, Clone Assay

    40) Product Images from "Constructing TC-1-GLUC-LMP2 Model Tumor Cells to Evaluate the Anti-Tumor Effects of LMP2-Related Vaccines"

    Article Title: Constructing TC-1-GLUC-LMP2 Model Tumor Cells to Evaluate the Anti-Tumor Effects of LMP2-Related Vaccines

    Journal: Viruses

    doi: 10.3390/v10040145

    The LMP2 and GLuc detection result in TC-1-GLUC-LMP2 cells. ( A ) PCR results of LMP2 and GLuc amplification using the TC-1-GLUC-LMP2 cells genomic DNA as a template. M: DNA ladder; 1: TC-1-GLUC-LMP2 cells as template using primers for LMP2 ; 2: DNA of pVR-LMP2 plasmid; 3: genomic DNA of TC-1 cells; 4: TC-1-GLUC-LMP2 cells as template using primers for GLuc; 5: DNA of pCMV-Gaussia Luc; 6: genomic DNA of TC-1 cells; ( B ) RT-PCR results to verify GLuc and LMP2 mRNA expression. M: RNA ladder; 1: RT-PCR result using TC-1-GLUC-LMP2 as template amplifying LMP2 ; 2: 293 cells transfected with pVR-LMP2 as template amplifying LMP2 ; 3: TC-1 cells as template amplifying LMP2; 4: RT-PCR result using TC-1-GLUC-LMP2 as template amplifying GLuc ; 5: 293 cells transfected with pCMV-Gaussia Luc as template amplifying GLuc ; 6: TC-1 cells as template amplifying GLuc ; ( C ) Western blot results of LMP2 protein expression in TC-1-GLUC-LMP2 cells at different passages. M: PageRuler Prestained Protein Ladder; 1: Passage 1 TC-1-GLUC-LMP2 cells, LMP2 with a molecular weight of 55 KD; 2: Passage 10 TC-1-GLUC-LMP2 cells; 3: Passage 30 TC-1-GLUC-LMP2 cells; 4: TC-1 cells; ( D ) Identifying the stable expression of GLuc . The mean relative light unit (RLU) value of 10 4 TC-1-GLUC-LMP2 cells at passages 1, 10 and 30 were 7.44 × 10 5 , 7.63 × 10 5 and 7.34 × 10 5 . NS, no significant difference; each column represents mean ± SD ( n = 5) in ( D ).
    Figure Legend Snippet: The LMP2 and GLuc detection result in TC-1-GLUC-LMP2 cells. ( A ) PCR results of LMP2 and GLuc amplification using the TC-1-GLUC-LMP2 cells genomic DNA as a template. M: DNA ladder; 1: TC-1-GLUC-LMP2 cells as template using primers for LMP2 ; 2: DNA of pVR-LMP2 plasmid; 3: genomic DNA of TC-1 cells; 4: TC-1-GLUC-LMP2 cells as template using primers for GLuc; 5: DNA of pCMV-Gaussia Luc; 6: genomic DNA of TC-1 cells; ( B ) RT-PCR results to verify GLuc and LMP2 mRNA expression. M: RNA ladder; 1: RT-PCR result using TC-1-GLUC-LMP2 as template amplifying LMP2 ; 2: 293 cells transfected with pVR-LMP2 as template amplifying LMP2 ; 3: TC-1 cells as template amplifying LMP2; 4: RT-PCR result using TC-1-GLUC-LMP2 as template amplifying GLuc ; 5: 293 cells transfected with pCMV-Gaussia Luc as template amplifying GLuc ; 6: TC-1 cells as template amplifying GLuc ; ( C ) Western blot results of LMP2 protein expression in TC-1-GLUC-LMP2 cells at different passages. M: PageRuler Prestained Protein Ladder; 1: Passage 1 TC-1-GLUC-LMP2 cells, LMP2 with a molecular weight of 55 KD; 2: Passage 10 TC-1-GLUC-LMP2 cells; 3: Passage 30 TC-1-GLUC-LMP2 cells; 4: TC-1 cells; ( D ) Identifying the stable expression of GLuc . The mean relative light unit (RLU) value of 10 4 TC-1-GLUC-LMP2 cells at passages 1, 10 and 30 were 7.44 × 10 5 , 7.63 × 10 5 and 7.34 × 10 5 . NS, no significant difference; each column represents mean ± SD ( n = 5) in ( D ).

    Techniques Used: Polymerase Chain Reaction, Amplification, Plasmid Preparation, Reverse Transcription Polymerase Chain Reaction, Expressing, Transfection, Western Blot, Molecular Weight

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    Methylation:

    Article Title: Inhibition of LCMR1 and ATG12 by demethylation-activated miR-570-3p is involved in the anti-metastasis effects of metformin on human osteosarcoma
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    (A, B) Qubit DNA yields for fresh frozen tumor tissue (*), Fresh frozen normal tissue (**), Allprotect-treated tumor tissue, and Allprotect-treated normal tissue isolated using (A) Qiagen's QIAamp kit (B) Qiagen's AllPrep kit.

    Journal: Biopreservation and Biobanking

    Article Title: Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

    doi: 10.1089/bio.2011.0034

    Figure Lengend Snippet: (A, B) Qubit DNA yields for fresh frozen tumor tissue (*), Fresh frozen normal tissue (**), Allprotect-treated tumor tissue, and Allprotect-treated normal tissue isolated using (A) Qiagen's QIAamp kit (B) Qiagen's AllPrep kit.

    Article Snippet: The aims of this study were (1) to ascertain the quality of a representative portion (10%) of samples biobanked at SJHB utilizing a combination of quality control approaches utilized by established international biobanks, – (2) to assess the capacity of AllPrep (Qiagen) to simultaneously isolate RNA, DNA, and protein from tumor and normal breast tissues, (3) to compare AllPrep with dedicated RNA and DNA extraction kits, that is, RNEasy® (Qiagen, RNA isolation) and QIAamp® (Qiagen, DNA isolation), (4) to evaluate the effectiveness of Allprotect, a new RNA, DNA, and protein stabilizer, and (5) to assess the impact (if any) of presampling measures taken to maintain the pathological specimen's diagnostic integrity on the ultimate quality of RNA, DNA, and protein isolates.

    Techniques: Isolation

    DNA isolation using the QIAamp Kit

    Journal: Biopreservation and Biobanking

    Article Title: Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

    doi: 10.1089/bio.2011.0034

    Figure Lengend Snippet: DNA isolation using the QIAamp Kit

    Article Snippet: The aims of this study were (1) to ascertain the quality of a representative portion (10%) of samples biobanked at SJHB utilizing a combination of quality control approaches utilized by established international biobanks, – (2) to assess the capacity of AllPrep (Qiagen) to simultaneously isolate RNA, DNA, and protein from tumor and normal breast tissues, (3) to compare AllPrep with dedicated RNA and DNA extraction kits, that is, RNEasy® (Qiagen, RNA isolation) and QIAamp® (Qiagen, DNA isolation), (4) to evaluate the effectiveness of Allprotect, a new RNA, DNA, and protein stabilizer, and (5) to assess the impact (if any) of presampling measures taken to maintain the pathological specimen's diagnostic integrity on the ultimate quality of RNA, DNA, and protein isolates.

    Techniques: DNA Extraction

    Metformin up-regulates the expression of miR-570-3p by the demethylation of DNA in 143B and U2OS cells. a The CpG islands of miR-570-3p promoter regions and primer used for DNA methylation study. b Metformin treatment in 143B and U2OS cells significantly decreased DNA methylation levels at the CpG islands of miR-570-3p promoter regions

    Journal: Cell Death & Disease

    Article Title: Inhibition of LCMR1 and ATG12 by demethylation-activated miR-570-3p is involved in the anti-metastasis effects of metformin on human osteosarcoma

    doi: 10.1038/s41419-018-0620-z

    Figure Lengend Snippet: Metformin up-regulates the expression of miR-570-3p by the demethylation of DNA in 143B and U2OS cells. a The CpG islands of miR-570-3p promoter regions and primer used for DNA methylation study. b Metformin treatment in 143B and U2OS cells significantly decreased DNA methylation levels at the CpG islands of miR-570-3p promoter regions

    Article Snippet: The methylation levels of miR-570-3p promoter was analyzed by BSP. miR-570-3p DNA was extracted using a DNA kit (Qiagen 51306, Germany), and 2 μg of DNA was subjected to bisulfite conversion using an EpiTect Bisulfite Kit (59104, Qiagen, Germany) according to the manufacturer’s instructions.

    Techniques: Expressing, DNA Methylation Assay

    Sample collection, DNA isolation and shotgun metagenomic sequencing. ( A ) (I.) Sample collection: Vitreous body (intraocular body fluid) was collected through vitrectomy from 14 patients with endophthalmitis following cataract surgery (n = 7) and intravitreal injection (n = 7). As control, vitreous was collected from 7 patients without postoperative endophthalmitis during macula hole surgery. Six aliquots (3 sample pairs) were obtained from balanced salt solution (BSS) that is infused into the eye during vitrectomy. Three aliquots were collected from separate BSS bottles (BSS-B) and the second set of aliquots was collected from the vitrectomy surgical system (BSS-S) after it had passed through the vitrectomy infusion line, respectively. The samples were examined using (II.) Cultivation-based analyses and (III.) DNA isolation (2 methods) Metagenomic shotgun sequencing, including the examination of DNA extraction (blank) controls. A total of 62 samples were sequenced using Illumina MiSeq sequencing technology. ( B ) More details to steps (II.) and (III.): (II.) Cultivation-based analyses: Aliquots of the vitreous body fluid and balanced salt solution samples were subjected to cultivation-based analyses separately at the hospital and research laboratories. Obtained isolates were analyzed using mass spectrometry and whole genome sequencing. (III.) DNA isolation Metagenomic shotgun sequencing: Samples were extracted using two DNA isolation procedures: QIAamp DNA Mini Kit (QIA) and QIAamp UCP Pathogen Mini kit (UCP). A DNA extraction (blank) control was included at each round of DNA isolation, i.e. one DNA extraction control for 12–14 samples in total per extraction round (more vitreous samples were extracted than analyzed in this study). To verify the presence of the main microorganisms detected in the metagenomics analysis, the shotgun metagenomics reads were mapped to the genome assemblies of the isolates obtained from the vitreous samples. Not displayed here is the mapping of metagenomic shotgun reads to microbial reference genomes in the database (Provided in Fig. 4 ). As an additional verification, PCR analyses were carried out to detect the presence of the most abundant microorganisms in the vitreous samples using organism-specific primer sets.

    Journal: Scientific Reports

    Article Title: Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

    doi: 10.1038/s41598-018-22416-4

    Figure Lengend Snippet: Sample collection, DNA isolation and shotgun metagenomic sequencing. ( A ) (I.) Sample collection: Vitreous body (intraocular body fluid) was collected through vitrectomy from 14 patients with endophthalmitis following cataract surgery (n = 7) and intravitreal injection (n = 7). As control, vitreous was collected from 7 patients without postoperative endophthalmitis during macula hole surgery. Six aliquots (3 sample pairs) were obtained from balanced salt solution (BSS) that is infused into the eye during vitrectomy. Three aliquots were collected from separate BSS bottles (BSS-B) and the second set of aliquots was collected from the vitrectomy surgical system (BSS-S) after it had passed through the vitrectomy infusion line, respectively. The samples were examined using (II.) Cultivation-based analyses and (III.) DNA isolation (2 methods) Metagenomic shotgun sequencing, including the examination of DNA extraction (blank) controls. A total of 62 samples were sequenced using Illumina MiSeq sequencing technology. ( B ) More details to steps (II.) and (III.): (II.) Cultivation-based analyses: Aliquots of the vitreous body fluid and balanced salt solution samples were subjected to cultivation-based analyses separately at the hospital and research laboratories. Obtained isolates were analyzed using mass spectrometry and whole genome sequencing. (III.) DNA isolation Metagenomic shotgun sequencing: Samples were extracted using two DNA isolation procedures: QIAamp DNA Mini Kit (QIA) and QIAamp UCP Pathogen Mini kit (UCP). A DNA extraction (blank) control was included at each round of DNA isolation, i.e. one DNA extraction control for 12–14 samples in total per extraction round (more vitreous samples were extracted than analyzed in this study). To verify the presence of the main microorganisms detected in the metagenomics analysis, the shotgun metagenomics reads were mapped to the genome assemblies of the isolates obtained from the vitreous samples. Not displayed here is the mapping of metagenomic shotgun reads to microbial reference genomes in the database (Provided in Fig. 4 ). As an additional verification, PCR analyses were carried out to detect the presence of the most abundant microorganisms in the vitreous samples using organism-specific primer sets.

    Article Snippet: Isolation of DNA from complex samples DNA was isolated from 200 μl vitreous fluid and balanced salt solution samples using two different DNA isolation procedures, i) the QIAamp DNA Mini Kit (51304, Qiagen) and ii) the QIAamp UCP Pathogen Mini Kit (50214, Qiagen).

    Techniques: DNA Extraction, Sequencing, Injection, Shotgun Sequencing, Mass Spectrometry, Polymerase Chain Reaction

    Summary of cultivation-based, metagenomics and whole genome sequence analyses. Bacterial isolates were obtained at the hospital laboratory (1 st cultivation) from vitreous from endophthalmitis patients following cataract surgery (C1-7) and intravitreal injection (I1-7) and the taxonomic affiliation of the isolates were determined by MALDI-TOF mass spectrometry (MS). Vitreous was analyzed through metagenomics at the research laboratory using two DNA isolation methods (QIAamp DNA Mini Kit, QIA; QIAamp UCP Pathogen Mini kit, UCP) and the taxonomic affiliation of reads was determined. The detected amount of human DNA sequences in percent (%) is provided in the first column of the Metagenomics tab. In the horizontal bar charts, the taxonomic identity and relative fraction of microbial reads for the most abundant identified organisms based on the Kraken + Bracken analysis is indicated for both DNA isolation methods. The read counts for the most abundant organism according to the Kraken + Bracken (all reads) and BLASTN (forward read) analyses are indicated to the right. The read counts for the most abundant organisms per sample as determined by Kraken, Bracken and BLASTn analyses are available through figshare at https://figshare.com/s/5feabfad1d8c495bf7a3 . Bacterial isolates for some samples were obtained in a second round of cultivation at the research laboratory (2 nd cultivation) and one representative per colony morphotype per vitreous sample was subjected to MS and whole genome sequencing (WGS). The taxonomic affiliation of isolates was determined through classification of assembled genomes using a k-mer based approach and genomic MLST, and antibiotic resistance genes were identified using ResFinder. Furthermore, metagenomic assemblies were generated from the shotgun metagenomic reads and analyzed with regards to taxonomic affiliation and selected functional characteristics (Supplementary Table S6 ). A video summary is available from figshare at https://figshare.com/s/38fe043f6a8ef1710444 .

    Journal: Scientific Reports

    Article Title: Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

    doi: 10.1038/s41598-018-22416-4

    Figure Lengend Snippet: Summary of cultivation-based, metagenomics and whole genome sequence analyses. Bacterial isolates were obtained at the hospital laboratory (1 st cultivation) from vitreous from endophthalmitis patients following cataract surgery (C1-7) and intravitreal injection (I1-7) and the taxonomic affiliation of the isolates were determined by MALDI-TOF mass spectrometry (MS). Vitreous was analyzed through metagenomics at the research laboratory using two DNA isolation methods (QIAamp DNA Mini Kit, QIA; QIAamp UCP Pathogen Mini kit, UCP) and the taxonomic affiliation of reads was determined. The detected amount of human DNA sequences in percent (%) is provided in the first column of the Metagenomics tab. In the horizontal bar charts, the taxonomic identity and relative fraction of microbial reads for the most abundant identified organisms based on the Kraken + Bracken analysis is indicated for both DNA isolation methods. The read counts for the most abundant organism according to the Kraken + Bracken (all reads) and BLASTN (forward read) analyses are indicated to the right. The read counts for the most abundant organisms per sample as determined by Kraken, Bracken and BLASTn analyses are available through figshare at https://figshare.com/s/5feabfad1d8c495bf7a3 . Bacterial isolates for some samples were obtained in a second round of cultivation at the research laboratory (2 nd cultivation) and one representative per colony morphotype per vitreous sample was subjected to MS and whole genome sequencing (WGS). The taxonomic affiliation of isolates was determined through classification of assembled genomes using a k-mer based approach and genomic MLST, and antibiotic resistance genes were identified using ResFinder. Furthermore, metagenomic assemblies were generated from the shotgun metagenomic reads and analyzed with regards to taxonomic affiliation and selected functional characteristics (Supplementary Table S6 ). A video summary is available from figshare at https://figshare.com/s/38fe043f6a8ef1710444 .

    Article Snippet: Isolation of DNA from complex samples DNA was isolated from 200 μl vitreous fluid and balanced salt solution samples using two different DNA isolation procedures, i) the QIAamp DNA Mini Kit (51304, Qiagen) and ii) the QIAamp UCP Pathogen Mini Kit (50214, Qiagen).

    Techniques: Sequencing, Injection, Mass Spectrometry, DNA Extraction, Generated, Functional Assay

    Number of samples in which C. botulinum group III was detected using real-time PCR according to the DNA extraction kit used and the analyzed matrix. Total: number of samples analyzed per matrix. QA QIAamp ® DNA Mini Kit (QIAGEN Inc., Valencia, CA, USA), QF QIAamp ® Fast DNA Stool Mini Kit (QIAGEN Inc., Valencia, CA, USA), PS PowerSoil ® DNA isolation kit (Mo Bio Laboratories Inc., Carlsbad, CA, USA), NS NucleoSpin ® Soil (Macherey–Nagel, Duren, Germany)

    Journal: BMC Research Notes

    Article Title: Detection of Clostridium botulinum group III in environmental samples from farms by real-time PCR using four commercial DNA extraction kits

    doi: 10.1186/s13104-018-3549-5

    Figure Lengend Snippet: Number of samples in which C. botulinum group III was detected using real-time PCR according to the DNA extraction kit used and the analyzed matrix. Total: number of samples analyzed per matrix. QA QIAamp ® DNA Mini Kit (QIAGEN Inc., Valencia, CA, USA), QF QIAamp ® Fast DNA Stool Mini Kit (QIAGEN Inc., Valencia, CA, USA), PS PowerSoil ® DNA isolation kit (Mo Bio Laboratories Inc., Carlsbad, CA, USA), NS NucleoSpin ® Soil (Macherey–Nagel, Duren, Germany)

    Article Snippet: The following kits were evaluated: PowerSoil® DNA isolation kit (Mo Bio Laboratories Inc., Carlsbad, CA, USA), QIAamp® Fast DNA Stool Mini Kit and QIAamp® DNA Mini Kit (QIAGEN Inc., Valencia, CA, USA), and NucleoSpin® Soil (Macherey–Nagel, Duren, Germany).

    Techniques: Real-time Polymerase Chain Reaction, DNA Extraction