untreated mcf 7 adr  (Qiagen)

 
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    QIAquick Gel Extraction Kit
    Description:
    For gel extraction cleanup of up to 10 μg DNA 70 bp to 10 kb from enzymatic reactions Kit contents Qiagen QIAquick Gel Extraction Kit 50 rxns 30 to 50L Elution Volume 10g Binding Capacity DNA Sample Tube Format Silica Technology Manual Processing 70 bp to 10 kb Fragment Fast and Convenient Procedure For Gel Extraction Cleanup of up to 10μg DNA 70 bp to 10 kb from Enzymatic Reactions Includes 50 QIAquick Spin Columns Buffers Collection Tubes 2mL Benefits Up to 95 recovery of ready to use DNA Fast and convenient procedure Cleanup of DNA up to 10 kb in three easy steps Gel loading dye for convenient sample analysis
    Catalog Number:
    28704
    Price:
    118
    Category:
    QIAquick Gel Extraction Kit
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    Structured Review

    Qiagen untreated mcf 7 adr
    QIAquick Gel Extraction Kit
    For gel extraction cleanup of up to 10 μg DNA 70 bp to 10 kb from enzymatic reactions Kit contents Qiagen QIAquick Gel Extraction Kit 50 rxns 30 to 50L Elution Volume 10g Binding Capacity DNA Sample Tube Format Silica Technology Manual Processing 70 bp to 10 kb Fragment Fast and Convenient Procedure For Gel Extraction Cleanup of up to 10μg DNA 70 bp to 10 kb from Enzymatic Reactions Includes 50 QIAquick Spin Columns Buffers Collection Tubes 2mL Benefits Up to 95 recovery of ready to use DNA Fast and convenient procedure Cleanup of DNA up to 10 kb in three easy steps Gel loading dye for convenient sample analysis
    https://www.bioz.com/result/untreated mcf 7 adr/product/Qiagen
    Average 88 stars, based on 11572 article reviews
    Price from $9.99 to $1999.99
    untreated mcf 7 adr - by Bioz Stars, 2020-09
    88/100 stars

    Images

    1) Product Images from "Nanolipoparticles-mediated MDR1 siRNA delivery reduces doxorubicin resistance in breast cancer cells and silences MDR1 expression in xenograft model of human breast cancer"

    Article Title: Nanolipoparticles-mediated MDR1 siRNA delivery reduces doxorubicin resistance in breast cancer cells and silences MDR1 expression in xenograft model of human breast cancer

    Journal: Iranian Journal of Basic Medical Sciences

    doi:

    Relative mRNA levels for MDR1 in MCF-7/ADR human multidrug-resistant breast cancer cells. MCF-7/ADR Cells transfected with different formulations and incubated for 24 or 48 hr. MDR1 mRNA downregulation efficiency was calculated by comparing the MDR1 mRNA expression value in each transfected group to the untreated group. The MDR1 mRNA expression value was normalized to β-actin . Data are means±SEM. (n=3; * P
    Figure Legend Snippet: Relative mRNA levels for MDR1 in MCF-7/ADR human multidrug-resistant breast cancer cells. MCF-7/ADR Cells transfected with different formulations and incubated for 24 or 48 hr. MDR1 mRNA downregulation efficiency was calculated by comparing the MDR1 mRNA expression value in each transfected group to the untreated group. The MDR1 mRNA expression value was normalized to β-actin . Data are means±SEM. (n=3; * P

    Techniques Used: Transfection, Incubation, Expressing

    Relative mRNA levels for MDR1 in MCF-7/ADR human multidrug-resistant breast cancer cells and their parental cells MCF-7. The MDR1 mRNA expression value was normalized to β-actin . Data are means±SEM. (n = 3; *** P
    Figure Legend Snippet: Relative mRNA levels for MDR1 in MCF-7/ADR human multidrug-resistant breast cancer cells and their parental cells MCF-7. The MDR1 mRNA expression value was normalized to β-actin . Data are means±SEM. (n = 3; *** P

    Techniques Used: Expressing

    Western blot assay to determine the effect of MDR1 siRNA loaded nanoparticles on the P-gp expression. MCF-7/ADR Cells transfected with different formulations at the 100 nM and incubated for 48, 72 or 96 hr. P-gp downregulation efficiency was calculated by comparing the level of P-gp expression in each transfected group to the untreated group. (A) Top: P-glycoprotein was detected with C219 antibody. Bottom: The same membrane was reprobed with anti-actin antibody. (B) The quantitation of Western blot images carried out by using UVtec software and the protein levels were normalized against actin intensity. Data are means±SEM (n= 3; ** P
    Figure Legend Snippet: Western blot assay to determine the effect of MDR1 siRNA loaded nanoparticles on the P-gp expression. MCF-7/ADR Cells transfected with different formulations at the 100 nM and incubated for 48, 72 or 96 hr. P-gp downregulation efficiency was calculated by comparing the level of P-gp expression in each transfected group to the untreated group. (A) Top: P-glycoprotein was detected with C219 antibody. Bottom: The same membrane was reprobed with anti-actin antibody. (B) The quantitation of Western blot images carried out by using UVtec software and the protein levels were normalized against actin intensity. Data are means±SEM (n= 3; ** P

    Techniques Used: Western Blot, Expressing, Transfection, Incubation, Quantitation Assay, Software

    Enhancement of chemosensitivity to doxorubicin. Cytotoxicity of doxorubicin in MCF-7/ADR cells was assessed by MTT. Untransfected cells (control), cells transfected with liposomes containing MDR1 siRNA 100 nM (NLP siM, OFA siM) or cells transfected with empty NLP (NLP) or NLP containing control siRNA 100 nM (NLP siC) (as negative controls). After 48 hr, cells were incubated with 10 µM doxorubicin for 48 hr. Relative cell viability compared with control group has been reported. Data are means±SEM (n=3; ** P
    Figure Legend Snippet: Enhancement of chemosensitivity to doxorubicin. Cytotoxicity of doxorubicin in MCF-7/ADR cells was assessed by MTT. Untransfected cells (control), cells transfected with liposomes containing MDR1 siRNA 100 nM (NLP siM, OFA siM) or cells transfected with empty NLP (NLP) or NLP containing control siRNA 100 nM (NLP siC) (as negative controls). After 48 hr, cells were incubated with 10 µM doxorubicin for 48 hr. Relative cell viability compared with control group has been reported. Data are means±SEM (n=3; ** P

    Techniques Used: MTT Assay, Transfection, Incubation

    2) Product Images from "Rapid and Sensitive Detection of Yersinia pestis Using Amplification of Plague Diagnostic Bacteriophages Monitored by Real-Time PCR"

    Article Title: Rapid and Sensitive Detection of Yersinia pestis Using Amplification of Plague Diagnostic Bacteriophages Monitored by Real-Time PCR

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0011337

    Determination of lysis speed and burst sizes for bacteriophages ϕA1122, L-413C, and P2 vir1 on Y. pestis CO92 pgm − . Phage burst sizes (an average phage progeny produced by one bacterial cell) correspond to plateaus on the curves.
    Figure Legend Snippet: Determination of lysis speed and burst sizes for bacteriophages ϕA1122, L-413C, and P2 vir1 on Y. pestis CO92 pgm − . Phage burst sizes (an average phage progeny produced by one bacterial cell) correspond to plateaus on the curves.

    Techniques Used: Lysis, Produced

    Lytic properties of bacteriophages ϕA1122, L-413C, and P2 vir1 towards Y. pestis CO92 pgm − . The dynamics of lysis was determined in BHI broth at multiplicity of infection of 0.1. Optical density was normalized to the start of infection (1 on the Y axis corresponds to the initial OD 600 = 0.2).
    Figure Legend Snippet: Lytic properties of bacteriophages ϕA1122, L-413C, and P2 vir1 towards Y. pestis CO92 pgm − . The dynamics of lysis was determined in BHI broth at multiplicity of infection of 0.1. Optical density was normalized to the start of infection (1 on the Y axis corresponds to the initial OD 600 = 0.2).

    Techniques Used: Lysis, Infection

    3) Product Images from "Rapid and Sensitive Detection of Yersinia pestis Using Amplification of Plague Diagnostic Bacteriophages Monitored by Real-Time PCR"

    Article Title: Rapid and Sensitive Detection of Yersinia pestis Using Amplification of Plague Diagnostic Bacteriophages Monitored by Real-Time PCR

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0011337

    qPCR tests on simulated clinical human blood samples. A. Linear regression of ϕA1122 DNA concentration in blood diluted 1∶20 in comparison with SM buffer data. B. ϕA1122-based detection of Y. pestis in artificially contaminated blood diluted 10-fold with BHI broth. To calculate the actual bacterial loads in the undiluted blood samples, the CFU numbers shown should be multiplied by 10. The starting points of phage infection correspond to 100 PFU per 1 µl sample and are normalized to 10 0 = 1.
    Figure Legend Snippet: qPCR tests on simulated clinical human blood samples. A. Linear regression of ϕA1122 DNA concentration in blood diluted 1∶20 in comparison with SM buffer data. B. ϕA1122-based detection of Y. pestis in artificially contaminated blood diluted 10-fold with BHI broth. To calculate the actual bacterial loads in the undiluted blood samples, the CFU numbers shown should be multiplied by 10. The starting points of phage infection correspond to 100 PFU per 1 µl sample and are normalized to 10 0 = 1.

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay, Infection

    Dynamics of growth of phages ϕA1122 and L-413C on different concentrations of Y. pestis cells detected by qPCR. The starting points of phage infection correspond to 100 PFU per 1 µl sample and are normalized to 1. A. The titer rise of ϕA1122. B. L-413C amplification.
    Figure Legend Snippet: Dynamics of growth of phages ϕA1122 and L-413C on different concentrations of Y. pestis cells detected by qPCR. The starting points of phage infection correspond to 100 PFU per 1 µl sample and are normalized to 1. A. The titer rise of ϕA1122. B. L-413C amplification.

    Techniques Used: Real-time Polymerase Chain Reaction, Infection, Amplification

    Parameters of ϕA1122- and L-413C-based qPCR tests for phage DNA and live phage particles determined by linear regression method. A and B, standard curves plotted for DNA concentrations of ϕA1122 and L-413C, respectively. C and D, standard curves plotted for live phage particles of ϕA1122 and L-413C, respectively.
    Figure Legend Snippet: Parameters of ϕA1122- and L-413C-based qPCR tests for phage DNA and live phage particles determined by linear regression method. A and B, standard curves plotted for DNA concentrations of ϕA1122 and L-413C, respectively. C and D, standard curves plotted for live phage particles of ϕA1122 and L-413C, respectively.

    Techniques Used: Real-time Polymerase Chain Reaction

    4) Product Images from "Live Cell Monitoring of hiPSC Generation and Differentiation Using Differential Expression of Endogenous microRNAs"

    Article Title: Live Cell Monitoring of hiPSC Generation and Differentiation Using Differential Expression of Endogenous microRNAs

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0011834

    hiPSCs transduced with the reporter vector containing miRNA targets show differentiation-specific reporter expression in EBs. hESC (H1) and 4 different hiPSC clones (E/m#1, E/m#5, E/m#101, and hiPSC#19) were differentiated into EBs and maintained 25 days in IMDM containing 10% FBS. EBs were then dissociated with 0.25% trypsin/EDTA and the reporter expression was analyzed by flow cytometry. Histograms filled with black are undifferentiated controls. Histograms filled with blue (EGFP) and pink (mCherry) are differentiated cells, respectively. The numbers indicated in histogram show percentage of positive cells (EGFP) and negative cells (mCherry). MFI: mean fluorescence intensity. U: MFI of undifferentiated cells. D: MFI of differentiated cells.
    Figure Legend Snippet: hiPSCs transduced with the reporter vector containing miRNA targets show differentiation-specific reporter expression in EBs. hESC (H1) and 4 different hiPSC clones (E/m#1, E/m#5, E/m#101, and hiPSC#19) were differentiated into EBs and maintained 25 days in IMDM containing 10% FBS. EBs were then dissociated with 0.25% trypsin/EDTA and the reporter expression was analyzed by flow cytometry. Histograms filled with black are undifferentiated controls. Histograms filled with blue (EGFP) and pink (mCherry) are differentiated cells, respectively. The numbers indicated in histogram show percentage of positive cells (EGFP) and negative cells (mCherry). MFI: mean fluorescence intensity. U: MFI of undifferentiated cells. D: MFI of differentiated cells.

    Techniques Used: Transduction, Plasmid Preparation, Expressing, Clone Assay, Flow Cytometry, Cytometry, Fluorescence

    Transduction of the reporter vector containing miRNA targets does not grossly affect expression of hESC-specific markers. (A and B) Single-cell suspensions of hESC (H1), hiPSCs transduced with a lentiviral vector encoding EGFP miR-T/mCherry miR-T (E/m#1, E/m#5, and E/m#101) or untransduced (hiPSC#19) were analyzed for the expression of EGFP and mCherry (A) and that of hESC-specific markers (SSEA1, SSEA3, TRA1-60, and TRA-1-81) (B) by flow cytometry. The number (%) in each quadrant is listed on each plot. (C) hESCs (H1), hiPSCs transduced with a lentiviral vector encoding EGFP miR-T/mCherry miR-T (E/m#1, E/m#5, and E/m#101) or untransduced (hiPSC#19) were plated on poly-L-lysine and Matrigel coated glass coverslips and expanded for a week. Cells were then fixed with 1% formaldehyde, permeabilized with 0.2% Triton X-100 for 5 min on ice, and stained with anti-Nanog antibody and DyLight488 conjugated anti-rabbit IgGs. 7-amino-actinomycin D (7-AAD) was used for nuclear staining.
    Figure Legend Snippet: Transduction of the reporter vector containing miRNA targets does not grossly affect expression of hESC-specific markers. (A and B) Single-cell suspensions of hESC (H1), hiPSCs transduced with a lentiviral vector encoding EGFP miR-T/mCherry miR-T (E/m#1, E/m#5, and E/m#101) or untransduced (hiPSC#19) were analyzed for the expression of EGFP and mCherry (A) and that of hESC-specific markers (SSEA1, SSEA3, TRA1-60, and TRA-1-81) (B) by flow cytometry. The number (%) in each quadrant is listed on each plot. (C) hESCs (H1), hiPSCs transduced with a lentiviral vector encoding EGFP miR-T/mCherry miR-T (E/m#1, E/m#5, and E/m#101) or untransduced (hiPSC#19) were plated on poly-L-lysine and Matrigel coated glass coverslips and expanded for a week. Cells were then fixed with 1% formaldehyde, permeabilized with 0.2% Triton X-100 for 5 min on ice, and stained with anti-Nanog antibody and DyLight488 conjugated anti-rabbit IgGs. 7-amino-actinomycin D (7-AAD) was used for nuclear staining.

    Techniques Used: Transduction, Plasmid Preparation, Expressing, Flow Cytometry, Cytometry, Staining

    Molecular characterization of hiPSCs transduced with the reporter vector containing miRNA targets. Total RNA was isolated using QIAGEN's RNeasy Mini kit from HFFs transduced with (4Fs/HFF) or without 4 reprogramming factors (HFF), hESCs (H1), and 4 different hiPSC clones transduced with (E/m#1, E/m#5, and E/m#101) or without (hiPSC#19) the reporter vector encoding EGFP miR-T/mCherry miR-T. Total RNA (250 ng) was reverse-transcribed using QIAGEN's Omniscript reverse transcription kit and used as a template in subsequent PCR with 5-PRIME's HotMaster Taq DNA polymerase. PCR products were analyzed on a 2% agarose gel. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as an internal control.
    Figure Legend Snippet: Molecular characterization of hiPSCs transduced with the reporter vector containing miRNA targets. Total RNA was isolated using QIAGEN's RNeasy Mini kit from HFFs transduced with (4Fs/HFF) or without 4 reprogramming factors (HFF), hESCs (H1), and 4 different hiPSC clones transduced with (E/m#1, E/m#5, and E/m#101) or without (hiPSC#19) the reporter vector encoding EGFP miR-T/mCherry miR-T. Total RNA (250 ng) was reverse-transcribed using QIAGEN's Omniscript reverse transcription kit and used as a template in subsequent PCR with 5-PRIME's HotMaster Taq DNA polymerase. PCR products were analyzed on a 2% agarose gel. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as an internal control.

    Techniques Used: Transduction, Plasmid Preparation, Isolation, Clone Assay, Polymerase Chain Reaction, Agarose Gel Electrophoresis

    5) Product Images from "A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization"

    Article Title: A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization

    Journal: Antonie Van Leeuwenhoek

    doi: 10.1007/s10482-010-9450-4

    Primer systems used to characterize the identified region ( A ) and the composition of the IS blocks ( B ). A Upper line : inferred localization of IS elements and the relA / spoT region and PCR systems based on genomic information of strain 1609. IS: unassigned nucleotides in the 1609 genome which represent insertion sequences. Superscript 1 Numbers: primer systems, corresponding to primers shown in Table 3 (ps1 through ps15; ps15 not indicated here). PCR systems consisted of two PCR primers (e.g. 1: ps1-F/ps1-R, 2: ps2-F/ps2-R, etc.). *: ps10 amplifies ISRso3 . **: ps13 amplifies ISRso2s . Second line : Presence and absence of sequences in strain KZR-5 on the basis of PCR and hybridization. : The absence in strain KZR-5 was confirmed by Southern blot analysis using the corresponding PCR products of strain 1609 as DIG labeled DNA probes. B Insertion sequence (IS) regions determined by sequence analysis of PCR products of strains 715 and 1609 that were obtained with primer combinations ps9-F/ps11-R or ps6-F/ps14-R. The position of the sequencing primers (ps9-F, ps6-F, ps11-R, ps14-R and IS2/3) is indicated. Superscript 2 : IS regions correspond to the two IS regions, which are similar, shown in A (IS)
    Figure Legend Snippet: Primer systems used to characterize the identified region ( A ) and the composition of the IS blocks ( B ). A Upper line : inferred localization of IS elements and the relA / spoT region and PCR systems based on genomic information of strain 1609. IS: unassigned nucleotides in the 1609 genome which represent insertion sequences. Superscript 1 Numbers: primer systems, corresponding to primers shown in Table 3 (ps1 through ps15; ps15 not indicated here). PCR systems consisted of two PCR primers (e.g. 1: ps1-F/ps1-R, 2: ps2-F/ps2-R, etc.). *: ps10 amplifies ISRso3 . **: ps13 amplifies ISRso2s . Second line : Presence and absence of sequences in strain KZR-5 on the basis of PCR and hybridization. : The absence in strain KZR-5 was confirmed by Southern blot analysis using the corresponding PCR products of strain 1609 as DIG labeled DNA probes. B Insertion sequence (IS) regions determined by sequence analysis of PCR products of strains 715 and 1609 that were obtained with primer combinations ps9-F/ps11-R or ps6-F/ps14-R. The position of the sequencing primers (ps9-F, ps6-F, ps11-R, ps14-R and IS2/3) is indicated. Superscript 2 : IS regions correspond to the two IS regions, which are similar, shown in A (IS)

    Techniques Used: Polymerase Chain Reaction, Hybridization, Southern Blot, Labeling, Sequencing

    Detection of a deletion incurred in R. solanacearum biovar 2 strain KZR-5. A Localization of five sequences of strain 715 in the strain 1609 genome. The numbers 52–56 correspond to sequences of clones shown in Table 2 . The spoT-F and spoT-R: indicate primers used for PCR amplification of the relA/spoT 1.6 Kb fragment. Positions 1 and 1,461 of relA/spoT (RSIPO_04909) correspond to positions 238,741 and 237,281 in the genome of strain 1609. B Southern blot analysis of genomic DNA of different R. solanacearum strains after restriction with Pst I using a 1.6 Kb relA/spoT fragment as DNA probe. The R. solanacearum strains used for hybridization are indicated in the figure. Lane P is unlabeled DNA probe
    Figure Legend Snippet: Detection of a deletion incurred in R. solanacearum biovar 2 strain KZR-5. A Localization of five sequences of strain 715 in the strain 1609 genome. The numbers 52–56 correspond to sequences of clones shown in Table 2 . The spoT-F and spoT-R: indicate primers used for PCR amplification of the relA/spoT 1.6 Kb fragment. Positions 1 and 1,461 of relA/spoT (RSIPO_04909) correspond to positions 238,741 and 237,281 in the genome of strain 1609. B Southern blot analysis of genomic DNA of different R. solanacearum strains after restriction with Pst I using a 1.6 Kb relA/spoT fragment as DNA probe. The R. solanacearum strains used for hybridization are indicated in the figure. Lane P is unlabeled DNA probe

    Techniques Used: Clone Assay, Polymerase Chain Reaction, Amplification, Southern Blot, Hybridization

    6) Product Images from "PCR-Based Molecular Diagnosis of Hepatitis Virus (HBV and HDV) in HCV Infected Patients and Their Biochemical Study"

    Article Title: PCR-Based Molecular Diagnosis of Hepatitis Virus (HBV and HDV) in HCV Infected Patients and Their Biochemical Study

    Journal: Journal of Pathogens

    doi: 10.1155/2016/3219793

    A representative 1.5% agarose gel of PCR products for the detection of HBV in HCV positive patients. Lane M: DNA marker, lane 1: positive control (242 bp), lane 2: negative control, and lanes 3 to 7: patients positive for HBV DNA.
    Figure Legend Snippet: A representative 1.5% agarose gel of PCR products for the detection of HBV in HCV positive patients. Lane M: DNA marker, lane 1: positive control (242 bp), lane 2: negative control, and lanes 3 to 7: patients positive for HBV DNA.

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

    7) Product Images from "Metabolic engineering of CHO cells for the development of a robust protein production platform"

    Article Title: Metabolic engineering of CHO cells for the development of a robust protein production platform

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0181455

    Comparative fed batch study of mAb expression in CHO-PYC2 clone 12 and CHO-S control cells. (A) Cell density, ( B) Cell viability, ( C) Lactate profile ( D) Specific productivity and (E) Titer profile.
    Figure Legend Snippet: Comparative fed batch study of mAb expression in CHO-PYC2 clone 12 and CHO-S control cells. (A) Cell density, ( B) Cell viability, ( C) Lactate profile ( D) Specific productivity and (E) Titer profile.

    Techniques Used: Expressing

    Comparative glycoform analysis of mAb secreted from the clone expressing PYC2 gene and a set of control without PYC2 over-expression. Relative abundance of glycan composition of a mAb.
    Figure Legend Snippet: Comparative glycoform analysis of mAb secreted from the clone expressing PYC2 gene and a set of control without PYC2 over-expression. Relative abundance of glycan composition of a mAb.

    Techniques Used: Expressing, Over Expression

    Culture performance of the clone 12 expressing PYC2 and parental CHO cell in culture medium MamPF77, CDM4perMAB and Dynamis in batch mode. Graph representing culture profile: (A and D) Cell density, (B and E) cell viability, (C and F) lactate profile.
    Figure Legend Snippet: Culture performance of the clone 12 expressing PYC2 and parental CHO cell in culture medium MamPF77, CDM4perMAB and Dynamis in batch mode. Graph representing culture profile: (A and D) Cell density, (B and E) cell viability, (C and F) lactate profile.

    Techniques Used: Expressing

    A comparative shake flask fed-batch study of the screened clones expressing PYC2 gene. Graph representing culture profile: (A) Cell density ( B) cell viability ( C) lactate profile ( D) glucose consumption profile for PYC2-expressing cells in shake-flask culture.
    Figure Legend Snippet: A comparative shake flask fed-batch study of the screened clones expressing PYC2 gene. Graph representing culture profile: (A) Cell density ( B) cell viability ( C) lactate profile ( D) glucose consumption profile for PYC2-expressing cells in shake-flask culture.

    Techniques Used: Clone Assay, Expressing

    Culture performance of the clone#12 expressing PYC2 and parental CHO cell in shake flask fed-batch culture. Graph representing culture profile: (A) Cell density,( B) cell viability, ( C) Glutamine ( D) lactate and ( E) glucose consumption profiles.
    Figure Legend Snippet: Culture performance of the clone#12 expressing PYC2 and parental CHO cell in shake flask fed-batch culture. Graph representing culture profile: (A) Cell density,( B) cell viability, ( C) Glutamine ( D) lactate and ( E) glucose consumption profiles.

    Techniques Used: Expressing

    Cell pool generation and cell line development for PYC2 engineering. (A-D) Schematic diagram of two-phase selection of pMPYC transfected CHO cells with varying concentration of MTX and puromycin. ( B-D) Cell density, viability and lactate production profiles for stable pool 1B, pool 1C and pool 2D in fed-batch culture mode as a function of time. (E-F ) Flow diagram depicts the steps followed to obtain a clonal CHO cell line from the heterogeneous population of a stable pool. Flow-cytometry used to gate the healthy cells population and sort the single CHO cell in a 384 well plate. Live cell imager is used to monitor the clonality and growth of the colony/cell in the consecutive days. Single clones are expanded from 384 well plates to T25 flask.
    Figure Legend Snippet: Cell pool generation and cell line development for PYC2 engineering. (A-D) Schematic diagram of two-phase selection of pMPYC transfected CHO cells with varying concentration of MTX and puromycin. ( B-D) Cell density, viability and lactate production profiles for stable pool 1B, pool 1C and pool 2D in fed-batch culture mode as a function of time. (E-F ) Flow diagram depicts the steps followed to obtain a clonal CHO cell line from the heterogeneous population of a stable pool. Flow-cytometry used to gate the healthy cells population and sort the single CHO cell in a 384 well plate. Live cell imager is used to monitor the clonality and growth of the colony/cell in the consecutive days. Single clones are expanded from 384 well plates to T25 flask.

    Techniques Used: Selection, Transfection, Concentration Assay, Flow Cytometry, Cytometry, Clone Assay

    Gene copy number and mRNA expression analysis of the PYC2 expressing clones. (A) Fold expression of the PYC2 m-RNA relative to the house keeping β-actin gene (cDNA used as a template). ( B) Calculation of gene copies relative to house-keeping β-actin gene for selected PYC2 clone#12 (genomic DNA used as a template).
    Figure Legend Snippet: Gene copy number and mRNA expression analysis of the PYC2 expressing clones. (A) Fold expression of the PYC2 m-RNA relative to the house keeping β-actin gene (cDNA used as a template). ( B) Calculation of gene copies relative to house-keeping β-actin gene for selected PYC2 clone#12 (genomic DNA used as a template).

    Techniques Used: Expressing

    8) Product Images from "De novo transcriptome assembly: a new laccase multigene family from the marine-derived basidiomycete Peniophora sp. CBMAI 1063"

    Article Title: De novo transcriptome assembly: a new laccase multigene family from the marine-derived basidiomycete Peniophora sp. CBMAI 1063

    Journal: AMB Express

    doi: 10.1186/s13568-017-0526-7

    Predicted amino acid sequence alignments of all 10 putative laccases from  Peniophora  sp. CBMAI 1063. Amino acids with 100% matches are highlighted in black. Numbers above the amino acids indicate that they are copper ion-bound. Dots below the amino acids indicate conserved regions in the fungal laccases (L1, L2, L3 and L4)
    Figure Legend Snippet: Predicted amino acid sequence alignments of all 10 putative laccases from Peniophora sp. CBMAI 1063. Amino acids with 100% matches are highlighted in black. Numbers above the amino acids indicate that they are copper ion-bound. Dots below the amino acids indicate conserved regions in the fungal laccases (L1, L2, L3 and L4)

    Techniques Used: Sequencing

    9) Product Images from "Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites"

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites

    Journal: Parasites & Vectors

    doi: 10.1186/s13071-017-1975-1

    Determination of in vitro transcribed RNAs and VLPs by agarose gel electrophoresis. a Agarose gel electrophoresis of in vitro transcribed RNAs. The size of the in vitro transcribed RNAs were marked above each lane and compared with a RNA marker (Thermo Fisher). b RNase A and DNase I digestion of VLPs. Lane 1: PET-MS2 (RNase A); Lane 2: PET-MS2 (DNase I); Lane 3: PET-MS2 (RNase A + DNase I); Lane 4: PET-MS2; Lane 5: YFV VLP(RNase A); Lane 6: YFV VLP (DNase I); Lane 7: YFV VLP (RNase A + DNase I); Lane 8: YFV VLP; Lane 9: EEEV VLP (RNase A); Lane 10: EEEV VLP (DNase I); Lane 11: EEEV VLP (RNase A + DNase I); Lane 12: EEEV VLP. The size of VLPs are compared to a DNA marker (TaKaRa). The nucleic acids between 1,000–2,000 bp are resistant to both RNase A and DNase I due to their packaging in the internal section of the VLPs
    Figure Legend Snippet: Determination of in vitro transcribed RNAs and VLPs by agarose gel electrophoresis. a Agarose gel electrophoresis of in vitro transcribed RNAs. The size of the in vitro transcribed RNAs were marked above each lane and compared with a RNA marker (Thermo Fisher). b RNase A and DNase I digestion of VLPs. Lane 1: PET-MS2 (RNase A); Lane 2: PET-MS2 (DNase I); Lane 3: PET-MS2 (RNase A + DNase I); Lane 4: PET-MS2; Lane 5: YFV VLP(RNase A); Lane 6: YFV VLP (DNase I); Lane 7: YFV VLP (RNase A + DNase I); Lane 8: YFV VLP; Lane 9: EEEV VLP (RNase A); Lane 10: EEEV VLP (DNase I); Lane 11: EEEV VLP (RNase A + DNase I); Lane 12: EEEV VLP. The size of VLPs are compared to a DNA marker (TaKaRa). The nucleic acids between 1,000–2,000 bp are resistant to both RNase A and DNase I due to their packaging in the internal section of the VLPs

    Techniques Used: In Vitro, Agarose Gel Electrophoresis, Marker, Positron Emission Tomography

    10) Product Images from "Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize"

    Article Title: Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize

    Journal: Plant Methods

    doi: 10.1186/s13007-016-0152-4

    Agarose gel electrophoresis showing genomic DNA preparation of two Z. mays hybrids M10 ( lanes 1 – 4 ) and M321 ( lanes 5 – 8 ). DNA extractions using the Mericon extraction method with different agarose concentrations, 1% ( a ), 1.5% ( b ) and 2% g agarose ( c ), lane− empty, lane+ positive Probe NTC. M A: λ DNA- HindIII marker, M B and C: one Kb Marker
    Figure Legend Snippet: Agarose gel electrophoresis showing genomic DNA preparation of two Z. mays hybrids M10 ( lanes 1 – 4 ) and M321 ( lanes 5 – 8 ). DNA extractions using the Mericon extraction method with different agarose concentrations, 1% ( a ), 1.5% ( b ) and 2% g agarose ( c ), lane− empty, lane+ positive Probe NTC. M A: λ DNA- HindIII marker, M B and C: one Kb Marker

    Techniques Used: Agarose Gel Electrophoresis, Marker

    Nano-Drop measurement profile of genomic DNA extractions from Z. mays . DNA extractions using a Qiagen extraction method. Probe = Sample
    Figure Legend Snippet: Nano-Drop measurement profile of genomic DNA extractions from Z. mays . DNA extractions using a Qiagen extraction method. Probe = Sample

    Techniques Used:

    Nano-Drop measurement profile of genomic DNA extractions from Z. mays . DNA extractions using Mericon extraction method. Probe = Sample
    Figure Legend Snippet: Nano-Drop measurement profile of genomic DNA extractions from Z. mays . DNA extractions using Mericon extraction method. Probe = Sample

    Techniques Used:

    11) Product Images from "Nuclear import of cutaneous beta genus HPV8 E7 oncoprotein is mediated by hydrophobic interactions between its zinc-binding domain and FG nucleoporins"

    Article Title: Nuclear import of cutaneous beta genus HPV8 E7 oncoprotein is mediated by hydrophobic interactions between its zinc-binding domain and FG nucleoporins

    Journal: Virology

    doi: 10.1016/j.virol.2013.11.020

    Kap β2 in excess competes with GST-8E7 for nuclear import Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), M9-GST (panels E and G) or GST (panels I and K) in the presence of HeLa cytosol, or Hela cytosol plus Kap β2 in excess. Panels A, C, E, G, I and K show the protein localization and panels B, D, F, H, J and L the DAPI staining of the nuclei. Note the nuclear import of GST-8E7 in panel A and its inhibition in panel C.
    Figure Legend Snippet: Kap β2 in excess competes with GST-8E7 for nuclear import Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), M9-GST (panels E and G) or GST (panels I and K) in the presence of HeLa cytosol, or Hela cytosol plus Kap β2 in excess. Panels A, C, E, G, I and K show the protein localization and panels B, D, F, H, J and L the DAPI staining of the nuclei. Note the nuclear import of GST-8E7 in panel A and its inhibition in panel C.

    Techniques Used: Incubation, Staining, Inhibition

    An antibody to Nup62 FG repeats domain inhibits the nuclear import of HPV8 E7 Digitonin-permeabilized HeLa cells were incubated with GST-8E7 in the presence of only transport buffer (panel A), or HeLa cytosol (panel B) or HeLa cytosol plus anti-Nup62 antibody (panel C), or with GST in the presence of HeLa cytosol (panel D). Note the nuclear import of GST-8E7 in panel B and its inhibition in panel C. The negative control GST was not imported into the nucleus in the presence of HeLa cytosol (panel D). Panels E-H represent the DAPI staining of the nuclei.
    Figure Legend Snippet: An antibody to Nup62 FG repeats domain inhibits the nuclear import of HPV8 E7 Digitonin-permeabilized HeLa cells were incubated with GST-8E7 in the presence of only transport buffer (panel A), or HeLa cytosol (panel B) or HeLa cytosol plus anti-Nup62 antibody (panel C), or with GST in the presence of HeLa cytosol (panel D). Note the nuclear import of GST-8E7 in panel B and its inhibition in panel C. The negative control GST was not imported into the nucleus in the presence of HeLa cytosol (panel D). Panels E-H represent the DAPI staining of the nuclei.

    Techniques Used: Incubation, Inhibition, Negative Control, Staining

    Mutation of hydrophobic residues within the zinc-binding domain disrupts the nuclear import of HPV8 E7 oncoprotein Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), GST-8E7 LRLFV65AAAAA (panels E and G), GST-8E7 R66A (panels I and K) and GST (panels M and O), in the presence of only transport buffer (panels A, E, I, and M) or HeLa cytosol and energy mix (panels C, G, K and O). Panels A, C, E, G, I, K, M and O show the protein localization and panels B, D, F, H, J, L, N and P the DAPI staining of the nuclei.
    Figure Legend Snippet: Mutation of hydrophobic residues within the zinc-binding domain disrupts the nuclear import of HPV8 E7 oncoprotein Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), GST-8E7 LRLFV65AAAAA (panels E and G), GST-8E7 R66A (panels I and K) and GST (panels M and O), in the presence of only transport buffer (panels A, E, I, and M) or HeLa cytosol and energy mix (panels C, G, K and O). Panels A, C, E, G, I, K, M and O show the protein localization and panels B, D, F, H, J, L, N and P the DAPI staining of the nuclei.

    Techniques Used: Mutagenesis, Binding Assay, Incubation, Staining

    GST-8E7 and GST-8cE7 are imported into the nuclei of digitonin-permeabilized HeLa cells Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), GST-8nE7 (panels E and G), GST-8cE7 (panels I and K), M9-GST (panels M and O) and GST (panels Q and S) in the presence of either transport buffer (A, E, I, M, and Q) or exogenous HeLa cytosol (panels C, G, K, O and S). Protein localization was detected with an anti-GST antibody. Panels A, C, E, G, I, K, M, O, Q and S show the protein localization and panels B, D, F, H, J, L, N, P, R and T the DAPI staining of the nuclei.
    Figure Legend Snippet: GST-8E7 and GST-8cE7 are imported into the nuclei of digitonin-permeabilized HeLa cells Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), GST-8nE7 (panels E and G), GST-8cE7 (panels I and K), M9-GST (panels M and O) and GST (panels Q and S) in the presence of either transport buffer (A, E, I, M, and Q) or exogenous HeLa cytosol (panels C, G, K, O and S). Protein localization was detected with an anti-GST antibody. Panels A, C, E, G, I, K, M, O, Q and S show the protein localization and panels B, D, F, H, J, L, N, P, R and T the DAPI staining of the nuclei.

    Techniques Used: Incubation, Staining

    The C91A mutation disrupts the nuclear import of GST-8E7 Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), GST-8E7 C91A (panels E and G), M9-GST (panels I and K) and GST (panels M and O) in the presence of either transport buffer (panels A, E, I and M) or exogenous HeLa cytosol (panels C, G, K and O). Protein localization was detected with an anti-GST antibody. Panels A, C, E, G, I, K, M and O show the protein localization and panels B, D, F, H, J, L, N and P the DAPI staining of the nuclei.
    Figure Legend Snippet: The C91A mutation disrupts the nuclear import of GST-8E7 Digitonin-permeabilized HeLa cells were incubated with GST-8E7 (panels A and C), GST-8E7 C91A (panels E and G), M9-GST (panels I and K) and GST (panels M and O) in the presence of either transport buffer (panels A, E, I and M) or exogenous HeLa cytosol (panels C, G, K and O). Protein localization was detected with an anti-GST antibody. Panels A, C, E, G, I, K, M and O show the protein localization and panels B, D, F, H, J, L, N and P the DAPI staining of the nuclei.

    Techniques Used: Mutagenesis, Incubation, Staining

    12) Product Images from "Improved reverse transcription-polymerase chain reaction assay for the detection of flaviviruses with semi-nested primers for discrimination between dengue virus serotypes and Zika virus"

    Article Title: Improved reverse transcription-polymerase chain reaction assay for the detection of flaviviruses with semi-nested primers for discrimination between dengue virus serotypes and Zika virus

    Journal: Memórias do Instituto Oswaldo Cruz

    doi: 10.1590/0074-02760170393

    : evaluation of the semi-nested polymerase chain reaction (PCR) for identification of dengue virus (DENV)1-4 serotypes and Zika virus (ZIKV). The efficiency of the semi-nested reaction using the primers DENV1F6.2, DENV2F10, DENV3F6.1, DENV4F3, ZIKVF8, and CRNS5_7NR6 was evaluated under different conditions. (A) Size resolution of each amplicon in a 2% agarose gel. The letters above each lane indicate the templates containing RNA of DENV serotypes (D1, D2, D3, and D4) or ZIKV (Z). The results of semi-nested reactions containing each primer individually and a template positive for Chikungunya virus are presented (below). (B) Tests using a mixture of reverse-transcribed RNAs as the template from two types of viruses. All possible combinations among the five viruses have been evaluated and are shown above each their respective gel lanes. The size of each amplicon in the 2% agarose gel are indicated (black arrows). (C) Dilution test to verify the sensitivity of the semi-nested reaction. L = 100 bp size marker.
    Figure Legend Snippet: : evaluation of the semi-nested polymerase chain reaction (PCR) for identification of dengue virus (DENV)1-4 serotypes and Zika virus (ZIKV). The efficiency of the semi-nested reaction using the primers DENV1F6.2, DENV2F10, DENV3F6.1, DENV4F3, ZIKVF8, and CRNS5_7NR6 was evaluated under different conditions. (A) Size resolution of each amplicon in a 2% agarose gel. The letters above each lane indicate the templates containing RNA of DENV serotypes (D1, D2, D3, and D4) or ZIKV (Z). The results of semi-nested reactions containing each primer individually and a template positive for Chikungunya virus are presented (below). (B) Tests using a mixture of reverse-transcribed RNAs as the template from two types of viruses. All possible combinations among the five viruses have been evaluated and are shown above each their respective gel lanes. The size of each amplicon in the 2% agarose gel are indicated (black arrows). (C) Dilution test to verify the sensitivity of the semi-nested reaction. L = 100 bp size marker.

    Techniques Used: Nested PCR, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Marker

    13) Product Images from "Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize"

    Article Title: Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

    Journal: Genetics

    doi: 10.1534/genetics.111.136176

    Genomic and RT–PCR analysis of Helitron Hel1-331 . (A) PCR product amplified from genomic DNA extracted from different maize inbred lines using primers, H31-1F and H31-1R, flanking the 5′ and 3′ sequence of the Helitron insertion, respectively. (B) RT–PCR products amplified from root and shoot tissues of maize inbred lines B73 and Mo17 using primers, H31E1F and H31E7R. (C) Splice alignment of the sequences of the RT–PCR products shown in B with the Helitron Hel1-331 sequence. The exons of a captured hypothetical gene, gi: 212721678, and an uncharacterized gene, are color coded in orange and yellow, respectively. In the alignment, boxes and lines denote exons and introns, respectively. Alternative donor and acceptor splice sites are joined by dashed lines and * marks the position of the retained introns. The size of the transcripts and the A and T nucleotides flanking the insertion site of the Helitron are indicated.
    Figure Legend Snippet: Genomic and RT–PCR analysis of Helitron Hel1-331 . (A) PCR product amplified from genomic DNA extracted from different maize inbred lines using primers, H31-1F and H31-1R, flanking the 5′ and 3′ sequence of the Helitron insertion, respectively. (B) RT–PCR products amplified from root and shoot tissues of maize inbred lines B73 and Mo17 using primers, H31E1F and H31E7R. (C) Splice alignment of the sequences of the RT–PCR products shown in B with the Helitron Hel1-331 sequence. The exons of a captured hypothetical gene, gi: 212721678, and an uncharacterized gene, are color coded in orange and yellow, respectively. In the alignment, boxes and lines denote exons and introns, respectively. Alternative donor and acceptor splice sites are joined by dashed lines and * marks the position of the retained introns. The size of the transcripts and the A and T nucleotides flanking the insertion site of the Helitron are indicated.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, Sequencing

    14) Product Images from "Techniques for the Isolation of High-Quality RNA from Cells Encapsulated in Chitosan Hydrogels"

    Article Title: Techniques for the Isolation of High-Quality RNA from Cells Encapsulated in Chitosan Hydrogels

    Journal: Tissue Engineering. Part C, Methods

    doi: 10.1089/ten.tec.2012.0693

    Representative end-point RT-PCR gene expression results for (a) 18S and (b) TfR from RNA isolated using the freeze grind+CTAB+RNeasy ® (FCR) method, the mince+CTAB+RNeasy ® (MCR) method, and the lysozyme+CTAB+RNeasy ® (LCR) method. Genomic contamination was detected following agarose gel electrophoresis in all minus-RT controls. In addition, as shown in the TfR results, where the primers were designed to span an intron–exon boundary, two products were formed during the PCR, corresponding to a genomic product size of 270 bp and an mRNA product size of 62 bp.
    Figure Legend Snippet: Representative end-point RT-PCR gene expression results for (a) 18S and (b) TfR from RNA isolated using the freeze grind+CTAB+RNeasy ® (FCR) method, the mince+CTAB+RNeasy ® (MCR) method, and the lysozyme+CTAB+RNeasy ® (LCR) method. Genomic contamination was detected following agarose gel electrophoresis in all minus-RT controls. In addition, as shown in the TfR results, where the primers were designed to span an intron–exon boundary, two products were formed during the PCR, corresponding to a genomic product size of 270 bp and an mRNA product size of 62 bp.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Expressing, Isolation, Agarose Gel Electrophoresis, Polymerase Chain Reaction

    15) Product Images from "Filter paper-based spin column method for cost-efficient DNA or RNA purification"

    Article Title: Filter paper-based spin column method for cost-efficient DNA or RNA purification

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0203011

    The efficiency of filter paper for purification of nucleic acids from various sources using respective Qiagen kits. (A) Tomato genomic DNAs purified using Qiagen DNeasy plant mini kit. (B) Tomato total RNAs purified using Qiagen RNeasy plant mini kit. (C) PCR products of a GUS fragment purified using Qiagen QIAquick PCR purification kit. (D) PCR products of GUS fragment recovered from an agarose gel using a Qiagen QIAquick gel extraction kit. (E) pUC -19 plasmid DNAs purified using a Qiagen QIAprep spin miniprep kit. For each panel, from left to right are (Q) nucleic acid purified in experiments using original Qiagen spin column, (G) reassembled spin column using two layers of Whatman glass microfiber filters (Grade GF/F), and (P) reassembled spin column using two layers of Whatman qualitative filter paper, (Grade 3) respectively. Upper panel is quantification data based on three experimental replicates normalized according to performance of the Qiagen kit; lower panel is an image of agarose gel electrophoresis for the same volume of purified nucleic acids.
    Figure Legend Snippet: The efficiency of filter paper for purification of nucleic acids from various sources using respective Qiagen kits. (A) Tomato genomic DNAs purified using Qiagen DNeasy plant mini kit. (B) Tomato total RNAs purified using Qiagen RNeasy plant mini kit. (C) PCR products of a GUS fragment purified using Qiagen QIAquick PCR purification kit. (D) PCR products of GUS fragment recovered from an agarose gel using a Qiagen QIAquick gel extraction kit. (E) pUC -19 plasmid DNAs purified using a Qiagen QIAprep spin miniprep kit. For each panel, from left to right are (Q) nucleic acid purified in experiments using original Qiagen spin column, (G) reassembled spin column using two layers of Whatman glass microfiber filters (Grade GF/F), and (P) reassembled spin column using two layers of Whatman qualitative filter paper, (Grade 3) respectively. Upper panel is quantification data based on three experimental replicates normalized according to performance of the Qiagen kit; lower panel is an image of agarose gel electrophoresis for the same volume of purified nucleic acids.

    Techniques Used: Purification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Gel Extraction, Plasmid Preparation

    Evaluation of purification of tobacco genomic DNA and total RNA using filter paper-based spin columns with respective Qiagen kit buffers and homemade buffers. (A) Agarose gel electrophoresis for 2.5 μl tobacco genomic DNAs elution from purification experiments using Qiagen DNeasy plant mini kit buffers with Qiagen original spin column (Lane Q/Q), filter paper recharged used spin column (Lane Q/R) and filter paper-based homemade spin column (Lane Q/H*), followed by tobacco genomic DNAs purified using homemade buffer with Qiagen original spin column (Lane H/Q), filter paper recharged used spin column (Lane H/R) and filter paper-based homemade spin column (Lane H/H*). (B) UV spectrum curve of tobacco DNAs purified using Qiagen kit (Q/Q, black curve), filter paper recharged spin columns with Qiagen kit buffers (Q/R, blue curve) or homemade buffers (H/R, red curve) from the same amount leaf tissue. Y-axis is UV absorbance, and X-axis is wavelength (nM). (C) Amplification plots for three duplicated qPCR reactions contain 20 ng DNA purified using Qiagen kit (Q/Q, Blue curves) or DNA purified from filter paper recharged spin column with homemade buffer (H/R, Red curves) respectively. The x-axis is PCR cycle numbers, Y-axis is the level of SYBR fluorescence, and the green line is an arbitrary threshold to determine the Cq value (the fractional cycle number at which amplification curve meet threshold level). (D) MOPS-formaldehyde denaturing agarose gel electrophoresis separated 5 μl RNA purified using Qiagen RNeasy plant mini kit buffers with a Qiagen original spin column (Lane Q/Q), filter paper recharged used spin column (Lane Q/R) and homemade filter paper-based spin column (Lane Q/H*), followed total tobacco RNAs purified by using homemade buffer with Qiagen original spin column (Lane H/Q), filter paper recharged used spin column (Lane H/R) and filter paper-based homemade spin column (Lane H/H*). (E) UV spectrum of tobacco total RNA purified using Qiagen kit (Q/Q, black curve), filter paper recharged spin column with Qiagen RNeasy plant mini kit buffers (Q/R, blue curve) or homemade buffers (H/R, red curve). Y-axis is UV absorbance, and the X-axis is wavelength. (F) Amplification plots of three duplicated qRT-PCR reactions for 2.5 ng RNA purified using Qiagen kit (Q/Q, Blue curves) or RNA purified using filter paper recharged spin column with homemade buffer (H/R, Red curves) respectively. Note: * The starting material amount is 100 mg tobacco leaf tissue for experiments using a Qiagen spin column or filter paper recharged spin column, and half amount of plant sample (50 mg) used for homemade spin column purification. All DNAs or RNAs were eluted using 100 ul elution solution.
    Figure Legend Snippet: Evaluation of purification of tobacco genomic DNA and total RNA using filter paper-based spin columns with respective Qiagen kit buffers and homemade buffers. (A) Agarose gel electrophoresis for 2.5 μl tobacco genomic DNAs elution from purification experiments using Qiagen DNeasy plant mini kit buffers with Qiagen original spin column (Lane Q/Q), filter paper recharged used spin column (Lane Q/R) and filter paper-based homemade spin column (Lane Q/H*), followed by tobacco genomic DNAs purified using homemade buffer with Qiagen original spin column (Lane H/Q), filter paper recharged used spin column (Lane H/R) and filter paper-based homemade spin column (Lane H/H*). (B) UV spectrum curve of tobacco DNAs purified using Qiagen kit (Q/Q, black curve), filter paper recharged spin columns with Qiagen kit buffers (Q/R, blue curve) or homemade buffers (H/R, red curve) from the same amount leaf tissue. Y-axis is UV absorbance, and X-axis is wavelength (nM). (C) Amplification plots for three duplicated qPCR reactions contain 20 ng DNA purified using Qiagen kit (Q/Q, Blue curves) or DNA purified from filter paper recharged spin column with homemade buffer (H/R, Red curves) respectively. The x-axis is PCR cycle numbers, Y-axis is the level of SYBR fluorescence, and the green line is an arbitrary threshold to determine the Cq value (the fractional cycle number at which amplification curve meet threshold level). (D) MOPS-formaldehyde denaturing agarose gel electrophoresis separated 5 μl RNA purified using Qiagen RNeasy plant mini kit buffers with a Qiagen original spin column (Lane Q/Q), filter paper recharged used spin column (Lane Q/R) and homemade filter paper-based spin column (Lane Q/H*), followed total tobacco RNAs purified by using homemade buffer with Qiagen original spin column (Lane H/Q), filter paper recharged used spin column (Lane H/R) and filter paper-based homemade spin column (Lane H/H*). (E) UV spectrum of tobacco total RNA purified using Qiagen kit (Q/Q, black curve), filter paper recharged spin column with Qiagen RNeasy plant mini kit buffers (Q/R, blue curve) or homemade buffers (H/R, red curve). Y-axis is UV absorbance, and the X-axis is wavelength. (F) Amplification plots of three duplicated qRT-PCR reactions for 2.5 ng RNA purified using Qiagen kit (Q/Q, Blue curves) or RNA purified using filter paper recharged spin column with homemade buffer (H/R, Red curves) respectively. Note: * The starting material amount is 100 mg tobacco leaf tissue for experiments using a Qiagen spin column or filter paper recharged spin column, and half amount of plant sample (50 mg) used for homemade spin column purification. All DNAs or RNAs were eluted using 100 ul elution solution.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Amplification, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Fluorescence, Quantitative RT-PCR

    16) Product Images from "Simultaneous Isolation of DNA and RNA from the Same Cell Population Obtained by Laser Capture Microdissection for Genome and Transcriptome Profiling"

    Article Title: Simultaneous Isolation of DNA and RNA from the Same Cell Population Obtained by Laser Capture Microdissection for Genome and Transcriptome Profiling

    Journal: The Journal of Molecular Diagnostics : JMD

    doi: 10.2353/jmoldx.2008.070131

    Using the DNA purified by the adapted AllPrep DNA/RNA method for genome profiling. A: Amplified tumor DNA fragments from DNA purified by the adapted AllPrep DNA/RNA method and by the QIAamp DNA purification method as revealed on a 2% agarose gel.
    Figure Legend Snippet: Using the DNA purified by the adapted AllPrep DNA/RNA method for genome profiling. A: Amplified tumor DNA fragments from DNA purified by the adapted AllPrep DNA/RNA method and by the QIAamp DNA purification method as revealed on a 2% agarose gel.

    Techniques Used: Purification, Amplification, DNA Purification, Agarose Gel Electrophoresis

    17) Product Images from "Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species"

    Article Title: Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

    Journal: Infection Ecology & Epidemiology

    doi: 10.1080/20008686.2017.1386536

    Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.
    Figure Legend Snippet: Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.

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

    Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.
    Figure Legend Snippet: Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.

    Techniques Used: Agarose Gel Electrophoresis

    18) Product Images from "Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species"

    Article Title: Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

    Journal: Infection Ecology & Epidemiology

    doi: 10.1080/20008686.2017.1386536

    Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.
    Figure Legend Snippet: Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.

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

    Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.
    Figure Legend Snippet: Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.

    Techniques Used: Agarose Gel Electrophoresis

    19) Product Images from "Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species"

    Article Title: Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

    Journal: Infection Ecology & Epidemiology

    doi: 10.1080/20008686.2017.1386536

    Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.
    Figure Legend Snippet: Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.

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

    Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.
    Figure Legend Snippet: Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.

    Techniques Used: Agarose Gel Electrophoresis

    20) Product Images from "Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species"

    Article Title: Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

    Journal: Infection Ecology & Epidemiology

    doi: 10.1080/20008686.2017.1386536

    Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.
    Figure Legend Snippet: Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.

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

    Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.
    Figure Legend Snippet: Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.

    Techniques Used: Agarose Gel Electrophoresis

    21) Product Images from "Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species"

    Article Title: Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

    Journal: Infection Ecology & Epidemiology

    doi: 10.1080/20008686.2017.1386536

    Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.
    Figure Legend Snippet: Agarose gel electrophoresis of C. jejuni -specific PCR with mallard eluates. (a) PCR products from DNA samples extracted with four different kits. Top row from left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit and DNeasy Blood Tissue Kit (sample S1). Bottom row from left: DNeasy Blood Tissue Kit (samples S2 and S3) and QIAamp cador Pathogen Kit. Faint bands were detected in samples extracted with DNeasy Blood Tissue kit and QIAamp cador Pathogen kit (bottom row). (b) Intense bands visible in samples pretreated with combined heat-shock and bead beating and extracted with the QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , consecutive samples. NC , negative control. PC , positive control.

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

    Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.
    Figure Legend Snippet: Agarose gel electrophoresis of kit eluates. (a) DNA yields after extraction with four different kits. From left: QIAamp Fast DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit, DNeasy Blood Tissue Kit and QIAamp cador Pathogen Kit. Faint smears observed in the DNeasy Blood Tissue kit and the QIAamp cador Pathogen kit lanes. (b) DNA yields after bead beating pretreatment and extraction with QIAamp cador Pathogen kit. L , DNA ladder. S1, S2 and S3 , fecal extracts.

    Techniques Used: Agarose Gel Electrophoresis

    22) 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

    23) Product Images from "Development and comprehensive characterization of porcine hepatocellular carcinoma for translational liver cancer investigation"

    Article Title: Development and comprehensive characterization of porcine hepatocellular carcinoma for translational liver cancer investigation

    Journal: Oncotarget

    doi: 10.18632/oncotarget.27647

    Oncopig intrahepatic HCC tumor formation. ( A ) Liver ultrasound depicting a hypoechoic 1 cm round intrahepatic HCC tumor (circled, L = liver, GB = gallbladder). ( B ) Contrast enhanced liver CT depicts same HCC tumor (circled). ( C ) Photograph of transected intrahepatic HCC tumor. ( D ) H E (20×) of Oncopig intrahepatic HCC tumor reveals architectural distortion characterized by expansion of liver cords, nuclear pleomorphism, anisonucleosis, and nodular fibrosis. Masson’s trichrome of adjacent non-tumorous liver demonstrates dense collagen bands (arrows) consistent with METAVIR grade 2-3 fibrosis. ( E ) Arginase-1 IHC (20×) shows patchy arginase-1 expression (brown) consistent with hepatocellular differentiation. KRAS G12D IHC (20×) confirms KRAS G12D expression (brown) consistent with malignancy.
    Figure Legend Snippet: Oncopig intrahepatic HCC tumor formation. ( A ) Liver ultrasound depicting a hypoechoic 1 cm round intrahepatic HCC tumor (circled, L = liver, GB = gallbladder). ( B ) Contrast enhanced liver CT depicts same HCC tumor (circled). ( C ) Photograph of transected intrahepatic HCC tumor. ( D ) H E (20×) of Oncopig intrahepatic HCC tumor reveals architectural distortion characterized by expansion of liver cords, nuclear pleomorphism, anisonucleosis, and nodular fibrosis. Masson’s trichrome of adjacent non-tumorous liver demonstrates dense collagen bands (arrows) consistent with METAVIR grade 2-3 fibrosis. ( E ) Arginase-1 IHC (20×) shows patchy arginase-1 expression (brown) consistent with hepatocellular differentiation. KRAS G12D IHC (20×) confirms KRAS G12D expression (brown) consistent with malignancy.

    Techniques Used: Immunohistochemistry, Expressing

    CRISPR/Cas9-mediated disruption of Oncopig KRAS G12D and TP53 R167H transgenes. ( A ) Schematic representation of the Oncopig transgene showing gRNA target sites and primers used for PCR. IRES, Internal ribosome entry site. ( B ) KRAS G12D and TP53 R167H editing efficiencies at multiple time points post transfection with Cas9 and gRNAs. ( C ) Frameshift mutations resulting in protein truncation for 2 Oncopig TP53 R167H KO HCC cell lines developed via single cell clone isolation and screening. Dashed line marks the cleavage position, and dashed grey boxes represent nucleotide deletions. Dotted regions represent frameshifts in predicted protein sequences. ( D ) Positive arginase-1 staining (brown) of parental and TP53 R167H KO cell lines (scale bar, 300 μm). ( E ) Cellular proliferation of Oncopig parental and TP53 R167H KO HCC cell lines. Values represent mean ± S. D. ( n ≥ 3). ** indicates P
    Figure Legend Snippet: CRISPR/Cas9-mediated disruption of Oncopig KRAS G12D and TP53 R167H transgenes. ( A ) Schematic representation of the Oncopig transgene showing gRNA target sites and primers used for PCR. IRES, Internal ribosome entry site. ( B ) KRAS G12D and TP53 R167H editing efficiencies at multiple time points post transfection with Cas9 and gRNAs. ( C ) Frameshift mutations resulting in protein truncation for 2 Oncopig TP53 R167H KO HCC cell lines developed via single cell clone isolation and screening. Dashed line marks the cleavage position, and dashed grey boxes represent nucleotide deletions. Dotted regions represent frameshifts in predicted protein sequences. ( D ) Positive arginase-1 staining (brown) of parental and TP53 R167H KO cell lines (scale bar, 300 μm). ( E ) Cellular proliferation of Oncopig parental and TP53 R167H KO HCC cell lines. Values represent mean ± S. D. ( n ≥ 3). ** indicates P

    Techniques Used: CRISPR, Polymerase Chain Reaction, Transfection, Isolation, Staining

    Oncopig, human, and murine HCC in vitro chemotherapeutic susceptibility. ( A ) Gene expression levels in Oncopig ( n = 3 cell lines) and human HCC cells (HepG2, Huh7, and Hep3B). ( B – F ) Correlation analysis of logIC 50 values demonstrating more similar in vitro chemotherapeutic responses between Oncopig and human compared to murine Hepa1-6 and human HCC cells. Chemotherapeutic response of each HCC cell line towards sorafenib, doxorubicin, cisplatin, mitomycin C, and 5-FU was determined. Pearson correlation between logIC 50 in Oncopig HCC cells or murine Hepa1-6 cells and the following human HCC cells was analyzed: (B) HepG2, (C) Hep3B, (D) Huh7, (E) SNU-387, and (F) SNU-475. * denotes P
    Figure Legend Snippet: Oncopig, human, and murine HCC in vitro chemotherapeutic susceptibility. ( A ) Gene expression levels in Oncopig ( n = 3 cell lines) and human HCC cells (HepG2, Huh7, and Hep3B). ( B – F ) Correlation analysis of logIC 50 values demonstrating more similar in vitro chemotherapeutic responses between Oncopig and human compared to murine Hepa1-6 and human HCC cells. Chemotherapeutic response of each HCC cell line towards sorafenib, doxorubicin, cisplatin, mitomycin C, and 5-FU was determined. Pearson correlation between logIC 50 in Oncopig HCC cells or murine Hepa1-6 cells and the following human HCC cells was analyzed: (B) HepG2, (C) Hep3B, (D) Huh7, (E) SNU-387, and (F) SNU-475. * denotes P

    Techniques Used: In Vitro, Expressing

    Oncopig HCC xenograft tumor development. ( A ) Representative SQ Oncopig HCC xenograft tumor. ( B ) Excised Oncopig HCC xenograft tumor. ( C ) H E (20×) of Oncopig HCC xenograft tumor reveals densely cellular subcutaneous nodule with interspersed fat cells. Intervening fibrous vascular septae noted. ( D ) On arginase-1 IHC (20×), epithelial cells show focal arginase-1 expression (brown) consistent with hepatocellular differentiation. ( E ) AFP expression across Oncopig HCC xenograft tumors ( n = 10).
    Figure Legend Snippet: Oncopig HCC xenograft tumor development. ( A ) Representative SQ Oncopig HCC xenograft tumor. ( B ) Excised Oncopig HCC xenograft tumor. ( C ) H E (20×) of Oncopig HCC xenograft tumor reveals densely cellular subcutaneous nodule with interspersed fat cells. Intervening fibrous vascular septae noted. ( D ) On arginase-1 IHC (20×), epithelial cells show focal arginase-1 expression (brown) consistent with hepatocellular differentiation. ( E ) AFP expression across Oncopig HCC xenograft tumors ( n = 10).

    Techniques Used: Immunohistochemistry, Expressing

    Oncopig SQ HCC autograft formation. ( A ) Photograph of visible SQ HCC tumor (circled) in Oncopig flank. ( B ) Excision of 2.0 cm SQ HCC tumor. ( C ) Excised and transected SQ HCC tumor. ( D ) H E (20×) of Oncopig SQ HCC tumor demonstrates prominent, dispersed, pleomorphic large atypical cells, 5–10× the size of lymphocytes, flanking fibrous vascular septae, surrounded by dense mixed immune cell infiltrates. Arginase-1 IHC (20×) shows that these atypical cells show patchy arginase-1 expression (brown) consistent with hepatocellular differentiation. KRAS G12D IHC (20×) confirms KRAS G12D expression (brown) consistent with malignancy. ( E ) AFP expression across Oncopig SQ HCC tumors ( n = 6).
    Figure Legend Snippet: Oncopig SQ HCC autograft formation. ( A ) Photograph of visible SQ HCC tumor (circled) in Oncopig flank. ( B ) Excision of 2.0 cm SQ HCC tumor. ( C ) Excised and transected SQ HCC tumor. ( D ) H E (20×) of Oncopig SQ HCC tumor demonstrates prominent, dispersed, pleomorphic large atypical cells, 5–10× the size of lymphocytes, flanking fibrous vascular septae, surrounded by dense mixed immune cell infiltrates. Arginase-1 IHC (20×) shows that these atypical cells show patchy arginase-1 expression (brown) consistent with hepatocellular differentiation. KRAS G12D IHC (20×) confirms KRAS G12D expression (brown) consistent with malignancy. ( E ) AFP expression across Oncopig SQ HCC tumors ( n = 6).

    Techniques Used: Immunohistochemistry, Expressing

    Genomic signatures of Oncopig HCC. ( A ) Somatic copy-number calling reveals a largely copy-neutral tumor in line with the young age of the tumor. ( B ) Representative venn diagram showing distribution of SNVs in the cell line and 2 out of 5 tumor samples. ( C ) Mutational signatures identified resemble signatures observed in human HCC tumors (Signatures 1, 12, and 17).
    Figure Legend Snippet: Genomic signatures of Oncopig HCC. ( A ) Somatic copy-number calling reveals a largely copy-neutral tumor in line with the young age of the tumor. ( B ) Representative venn diagram showing distribution of SNVs in the cell line and 2 out of 5 tumor samples. ( C ) Mutational signatures identified resemble signatures observed in human HCC tumors (Signatures 1, 12, and 17).

    Techniques Used:

    Oncopig and human HCC in vitro phenotypes. ( A ) Schematic of Oncopig transgene construct and agarose gel electrophoresis of RT-PCR products confirming Oncopig transgene ( KRAS G12D and TP53 R167H ) expression following exposure to AdCre. ( B ) Positive arginase-1 and KRAS G12D staining (brown) of cultured Oncopig HCC cell lines (20×). ( C ) Oncopig and human HCC cell cycle lengths. ( D ) Representative cell migration images depicting faster gap closure in Oncopig compared to HepG2 and half gap closure rates for Oncopig ( n = 15 cell lines) and human HCC cells. ( E ) AFP secretion from Oncopig ( n = 15 cell lines) and human HCC cells. Huh7, SNU-387, and SNU475 are known non-AFP producing cell lines. ns = non-significant, * denotes p -value
    Figure Legend Snippet: Oncopig and human HCC in vitro phenotypes. ( A ) Schematic of Oncopig transgene construct and agarose gel electrophoresis of RT-PCR products confirming Oncopig transgene ( KRAS G12D and TP53 R167H ) expression following exposure to AdCre. ( B ) Positive arginase-1 and KRAS G12D staining (brown) of cultured Oncopig HCC cell lines (20×). ( C ) Oncopig and human HCC cell cycle lengths. ( D ) Representative cell migration images depicting faster gap closure in Oncopig compared to HepG2 and half gap closure rates for Oncopig ( n = 15 cell lines) and human HCC cells. ( E ) AFP secretion from Oncopig ( n = 15 cell lines) and human HCC cells. Huh7, SNU-387, and SNU475 are known non-AFP producing cell lines. ns = non-significant, * denotes p -value

    Techniques Used: In Vitro, Construct, Agarose Gel Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Expressing, Staining, Cell Culture, Migration

    24) Product Images from "Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity"

    Article Title: Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity

    Journal: Folia Microbiologica

    doi: 10.1007/s12223-015-0385-z

    Dendrogram generated using Jaccard’s coefficient and the UPGMA clustering method. Binary matrices for T. atroviride strains were constructed based on evaluation of RAPD amplicons generated using 55 primers. Cluster analysis of the binary data was performed using NTSYS-pc 2.1 software. Similarity matrices were generated using Jaccard’s coefficient and an unweighted pair-group method using arithmetic averages (UPGMA) was used to generate the dendrogram
    Figure Legend Snippet: Dendrogram generated using Jaccard’s coefficient and the UPGMA clustering method. Binary matrices for T. atroviride strains were constructed based on evaluation of RAPD amplicons generated using 55 primers. Cluster analysis of the binary data was performed using NTSYS-pc 2.1 software. Similarity matrices were generated using Jaccard’s coefficient and an unweighted pair-group method using arithmetic averages (UPGMA) was used to generate the dendrogram

    Techniques Used: Generated, Construct, Software

    25) Product Images from "APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells"

    Article Title: APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells

    Journal: Scientific Reports

    doi: 10.1038/srep00806

    Foreign DNA editing by A3A, A3B, and AID. (A) Agarose gel analyses of 3D-PCR products from HEK293 cells. Cells were transfected with expression vector for A3A, A3B wild-type or mutant, or AID together with pEGFP-N3 and pEF-UGI. Total DNA was recovered 2 days after transfection, and EGFP gene was amplified by 3D-PCR at the indicated denaturation temperatures (Td). (B) Mutation matrices of hyperedited EGFP sequences derived from cloned amplicons at 83.8°C of Td. “n” indicates the number of bases sequenced. We sequenced 5 clones (2,225 base pairs in total) in each group. (C) Frequencies of C/G to T/A transitions in hyperedited EGFP genes. C/G to T/A transitions per 1,000 sequenced base pairs are shown. (D) Dinucleotide contexts in foreign DNA editing. The rates of indicated dinucleotide sequence at the C to T transitions are shown. Asterisks indicate statistical significance in a χ 2 test (p
    Figure Legend Snippet: Foreign DNA editing by A3A, A3B, and AID. (A) Agarose gel analyses of 3D-PCR products from HEK293 cells. Cells were transfected with expression vector for A3A, A3B wild-type or mutant, or AID together with pEGFP-N3 and pEF-UGI. Total DNA was recovered 2 days after transfection, and EGFP gene was amplified by 3D-PCR at the indicated denaturation temperatures (Td). (B) Mutation matrices of hyperedited EGFP sequences derived from cloned amplicons at 83.8°C of Td. “n” indicates the number of bases sequenced. We sequenced 5 clones (2,225 base pairs in total) in each group. (C) Frequencies of C/G to T/A transitions in hyperedited EGFP genes. C/G to T/A transitions per 1,000 sequenced base pairs are shown. (D) Dinucleotide contexts in foreign DNA editing. The rates of indicated dinucleotide sequence at the C to T transitions are shown. Asterisks indicate statistical significance in a χ 2 test (p

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Transfection, Expressing, Plasmid Preparation, Mutagenesis, Amplification, Derivative Assay, Clone Assay, Sequencing

    Expression of A3B and somatic mutations in oncogenes in human lymphoma cell lines. (A) Quantitative RT-PCR for A3A , A3B , and AID in lymphoma cell lines. The levels of target cDNA were normalized to the endogenous hypoxanthine phosphoribosyl transferase 1 ( HPRT1 ) and then compared to those in peripheral blood lymphocytes. (B) Mutational analyses of C-myc , Pax5 , and A20 in SUDH6 and KIS1 cells. We recovered total DNA from the cells and amplified the sequence between exon1 and intron1 of C-myc , Pax5 and A20 by PCR and performed direct sequencing of the amplicons. Locations of somatic mutations are shown below the loci with their positions. (C) The expression levels of transcripts of C-myc , Pax5 , and A20 in KIS1 and SUDHL6 cells. Quantitative RT-PCR was similarly performed with (a).
    Figure Legend Snippet: Expression of A3B and somatic mutations in oncogenes in human lymphoma cell lines. (A) Quantitative RT-PCR for A3A , A3B , and AID in lymphoma cell lines. The levels of target cDNA were normalized to the endogenous hypoxanthine phosphoribosyl transferase 1 ( HPRT1 ) and then compared to those in peripheral blood lymphocytes. (B) Mutational analyses of C-myc , Pax5 , and A20 in SUDH6 and KIS1 cells. We recovered total DNA from the cells and amplified the sequence between exon1 and intron1 of C-myc , Pax5 and A20 by PCR and performed direct sequencing of the amplicons. Locations of somatic mutations are shown below the loci with their positions. (C) The expression levels of transcripts of C-myc , Pax5 , and A20 in KIS1 and SUDHL6 cells. Quantitative RT-PCR was similarly performed with (a).

    Techniques Used: Expressing, Quantitative RT-PCR, Amplification, Sequencing, Polymerase Chain Reaction

    Deep sequencing of EGFP genes in genomic DNA. (A) The distributions of C/G to T/A substitutions in the EGFP sequences. Total DNA was recovered form HEK293/EGFP cells 7 days after transfection with expression vector for A3A, A3B wild type or H66/253R or AID. We amplified a portion of EGFP sequence from thymine 47 to cytidine 504 (top schematic) by PCR with high-fidelity polymerase and sequenced the amplicons by GS-junior bench top system (Roche). Sequence data were analyzed with equipped software. “Coverage” indicates the total numbers of sequenced reads. (B) Frequencies of base substitutions in hyperedited EGFP genes. Base substitutions were classified to 6 groups and substituted base number of each group per 1,000 sequenced base pairs are show. (C) Dinucleotide contexts in genomic DNA editing. The rates of indicated dinucleotide sequence at the C to T transitions are shown. Deviations in the editing contexts do not reach statistical significance (p
    Figure Legend Snippet: Deep sequencing of EGFP genes in genomic DNA. (A) The distributions of C/G to T/A substitutions in the EGFP sequences. Total DNA was recovered form HEK293/EGFP cells 7 days after transfection with expression vector for A3A, A3B wild type or H66/253R or AID. We amplified a portion of EGFP sequence from thymine 47 to cytidine 504 (top schematic) by PCR with high-fidelity polymerase and sequenced the amplicons by GS-junior bench top system (Roche). Sequence data were analyzed with equipped software. “Coverage” indicates the total numbers of sequenced reads. (B) Frequencies of base substitutions in hyperedited EGFP genes. Base substitutions were classified to 6 groups and substituted base number of each group per 1,000 sequenced base pairs are show. (C) Dinucleotide contexts in genomic DNA editing. The rates of indicated dinucleotide sequence at the C to T transitions are shown. Deviations in the editing contexts do not reach statistical significance (p

    Techniques Used: Sequencing, Transfection, Expressing, Plasmid Preparation, Amplification, Polymerase Chain Reaction, Software

    A3B induced somatic mutations into c-myc gene in human lymphoma cells. (A) Agarose gel analyses of 3D-PCR products of c-Myc genes in SUDHL6. We transfected expression vector for A3B wild-type or H66/253R or empty vector and recovered total DNA 7 days after transfection. C-myc genes were amplified by 3D-PCR at the indicated denaturation temperatures (Td). (B) Clonal sequencing of amplicons from A3B-WT expressing SUDHL6 cells. We sequenced 11 clones (5104 base pairs in total). Seventy six bases from thymine 310 to adenine 385 in which mutations are concentrated among sequenced 464 base pairs are shown. The numbers of C/G to T/A substitutions in sequenced 464 base pair length are shown at the right end. (C) Dinucleotide contexts of somatic mutations in c-Myc gene by A3B. The rates of indicated dinucleotide sequence at the C to T transitions are shown. Asterisks indicate statistical significance in a χ 2 test (p
    Figure Legend Snippet: A3B induced somatic mutations into c-myc gene in human lymphoma cells. (A) Agarose gel analyses of 3D-PCR products of c-Myc genes in SUDHL6. We transfected expression vector for A3B wild-type or H66/253R or empty vector and recovered total DNA 7 days after transfection. C-myc genes were amplified by 3D-PCR at the indicated denaturation temperatures (Td). (B) Clonal sequencing of amplicons from A3B-WT expressing SUDHL6 cells. We sequenced 11 clones (5104 base pairs in total). Seventy six bases from thymine 310 to adenine 385 in which mutations are concentrated among sequenced 464 base pairs are shown. The numbers of C/G to T/A substitutions in sequenced 464 base pair length are shown at the right end. (C) Dinucleotide contexts of somatic mutations in c-Myc gene by A3B. The rates of indicated dinucleotide sequence at the C to T transitions are shown. Asterisks indicate statistical significance in a χ 2 test (p

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Transfection, Expressing, Plasmid Preparation, Amplification, Sequencing, Clone Assay

    26) Product Images from "Rapid and Sensitive Detection of Yersinia pestis Using Amplification of Plague Diagnostic Bacteriophages Monitored by Real-Time PCR"

    Article Title: Rapid and Sensitive Detection of Yersinia pestis Using Amplification of Plague Diagnostic Bacteriophages Monitored by Real-Time PCR

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0011337

    Determination of lysis speed and burst sizes for bacteriophages ϕA1122, L-413C, and P2 vir1 on Y. pestis CO92 pgm − . Phage burst sizes (an average phage progeny produced by one bacterial cell) correspond to plateaus on the curves.
    Figure Legend Snippet: Determination of lysis speed and burst sizes for bacteriophages ϕA1122, L-413C, and P2 vir1 on Y. pestis CO92 pgm − . Phage burst sizes (an average phage progeny produced by one bacterial cell) correspond to plateaus on the curves.

    Techniques Used: Lysis, Produced

    Dynamics of growth of phages ϕA1122 and L-413C on different concentrations of Y. pestis cells detected by qPCR. The starting points of phage infection correspond to 100 PFU per 1 µl sample and are normalized to 1. A. The titer rise of ϕA1122. B. L-413C amplification.
    Figure Legend Snippet: Dynamics of growth of phages ϕA1122 and L-413C on different concentrations of Y. pestis cells detected by qPCR. The starting points of phage infection correspond to 100 PFU per 1 µl sample and are normalized to 1. A. The titer rise of ϕA1122. B. L-413C amplification.

    Techniques Used: Real-time Polymerase Chain Reaction, Infection, Amplification

    Parameters of ϕA1122- and L-413C-based qPCR tests for phage DNA and live phage particles determined by linear regression method. A and B, standard curves plotted for DNA concentrations of ϕA1122 and L-413C, respectively. C and D, standard curves plotted for live phage particles of ϕA1122 and L-413C, respectively.
    Figure Legend Snippet: Parameters of ϕA1122- and L-413C-based qPCR tests for phage DNA and live phage particles determined by linear regression method. A and B, standard curves plotted for DNA concentrations of ϕA1122 and L-413C, respectively. C and D, standard curves plotted for live phage particles of ϕA1122 and L-413C, respectively.

    Techniques Used: Real-time Polymerase Chain Reaction

    Lytic properties of bacteriophages ϕA1122, L-413C, and P2 vir1 towards Y. pestis CO92 pgm − . The dynamics of lysis was determined in BHI broth at multiplicity of infection of 0.1. Optical density was normalized to the start of infection (1 on the Y axis corresponds to the initial OD 600 = 0.2).
    Figure Legend Snippet: Lytic properties of bacteriophages ϕA1122, L-413C, and P2 vir1 towards Y. pestis CO92 pgm − . The dynamics of lysis was determined in BHI broth at multiplicity of infection of 0.1. Optical density was normalized to the start of infection (1 on the Y axis corresponds to the initial OD 600 = 0.2).

    Techniques Used: Lysis, Infection

    27) Product Images from "Encapsidation of Viral RNA in Picornavirales: Studies on Cowpea Mosaic Virus Demonstrate Dependence on Viral Replication"

    Article Title: Encapsidation of Viral RNA in Picornavirales: Studies on Cowpea Mosaic Virus Demonstrate Dependence on Viral Replication

    Journal: Journal of Virology

    doi: 10.1128/JVI.01520-18

    A replication-competent version of RNA-1 is necessary for RNA encapsidation. CPMV particles were purified from N. benthamiana leaves agroinfiltrated with pBinPS1NT and pBinPS2NT (lanes 1 in each gel), pBinPS1NT and pEAQ- HT -VP60 (lanes 2), pBinP32E and pBinPS2NT (lanes 3), and pBinP32E and pEAQ- HT -VP60 (lanes 4) or with pEAQ- HT -VP60 alone (lanes 5). In each case, the CPMV RNAs expressed within the leaves are indicated. The purified particles were examined by either denaturing SDS-PAGE followed by staining with Instant Blue (a) or electrophoresis on a nondenaturing agarose gel (b) followed by staining with either Instant Blue (left) to visualize protein or ethidium bromide (EtBr) (right) to visualize nucleic acid. The positions of the large (L) coat protein and two forms of the small [S (slow) and S (fast)] coat protein are indicated to the left of the gel in panel a. Note that in panel b, CPMV particles separate into distinct electrophoretic populations based on the presence or absence of the labile 24 amino acids at the C terminus of the small coat protein ( 2 ) as seen in panel a.
    Figure Legend Snippet: A replication-competent version of RNA-1 is necessary for RNA encapsidation. CPMV particles were purified from N. benthamiana leaves agroinfiltrated with pBinPS1NT and pBinPS2NT (lanes 1 in each gel), pBinPS1NT and pEAQ- HT -VP60 (lanes 2), pBinP32E and pBinPS2NT (lanes 3), and pBinP32E and pEAQ- HT -VP60 (lanes 4) or with pEAQ- HT -VP60 alone (lanes 5). In each case, the CPMV RNAs expressed within the leaves are indicated. The purified particles were examined by either denaturing SDS-PAGE followed by staining with Instant Blue (a) or electrophoresis on a nondenaturing agarose gel (b) followed by staining with either Instant Blue (left) to visualize protein or ethidium bromide (EtBr) (right) to visualize nucleic acid. The positions of the large (L) coat protein and two forms of the small [S (slow) and S (fast)] coat protein are indicated to the left of the gel in panel a. Note that in panel b, CPMV particles separate into distinct electrophoretic populations based on the presence or absence of the labile 24 amino acids at the C terminus of the small coat protein ( 2 ) as seen in panel a.

    Techniques Used: Purification, SDS Page, Staining, Electrophoresis, Agarose Gel Electrophoresis

    GDD mutants of RNA-1 are encapsidation deficient. Particles were purified from leaves agroinfiltrated with pEAQ-RNA-2 and an RNA-1-based construct, as indicated. The same preparation of purified particles was used for the gels shown here. (a) Protein content of particles visualized by SDS-PAGE and Instant Blue staining. The correctly processed large (L) coat protein and two electrophoretic forms of the small (S) coat protein present in all samples are indicated. (b) Purified particles from the same preparations as in panel a were analyzed in duplicate on a native agarose gel. (Left) Half of the gel was stained with Instant Blue protein stain to reveal equal loading of particles; (right) the other half of the gel was stained with ethidium bromide to visualize encapsidated nucleic acid. The positions of the L coat protein and two forms of the S coat protein are indicated to the left of the gel in panel a. Note that in panel b, CPMV particles separate into distinct electrophoretic populations based on the presence or absence of the labile 24 amino acids at the C terminus of the small coat protein ( 2 ) as seen in panel a. (c) RNA extracted from equal amounts of purified particles analyzed on an ethidium bromide-stained denaturing agarose RNA gel to reveal encapsidated RNA-1 and RNA-2. (d) Nucleic acid sequencing was carried out on the encapsidated RNA-1-Int-GAD seen in lane 2 in panel c, and this revealed that the encapsidated RNA has preserved the GAD mutation and has not reverted to wild-type GDD. Duplicate sequencing chromatograms are aligned to the wild-type sequence encoding GDD to highlight the point mutation, with the relevant amino acids indicated above. Sequencing was carried out by Eurofins Scientific, and sequence alignment was carried out using Vector NTI Advance 11.5.3.
    Figure Legend Snippet: GDD mutants of RNA-1 are encapsidation deficient. Particles were purified from leaves agroinfiltrated with pEAQ-RNA-2 and an RNA-1-based construct, as indicated. The same preparation of purified particles was used for the gels shown here. (a) Protein content of particles visualized by SDS-PAGE and Instant Blue staining. The correctly processed large (L) coat protein and two electrophoretic forms of the small (S) coat protein present in all samples are indicated. (b) Purified particles from the same preparations as in panel a were analyzed in duplicate on a native agarose gel. (Left) Half of the gel was stained with Instant Blue protein stain to reveal equal loading of particles; (right) the other half of the gel was stained with ethidium bromide to visualize encapsidated nucleic acid. The positions of the L coat protein and two forms of the S coat protein are indicated to the left of the gel in panel a. Note that in panel b, CPMV particles separate into distinct electrophoretic populations based on the presence or absence of the labile 24 amino acids at the C terminus of the small coat protein ( 2 ) as seen in panel a. (c) RNA extracted from equal amounts of purified particles analyzed on an ethidium bromide-stained denaturing agarose RNA gel to reveal encapsidated RNA-1 and RNA-2. (d) Nucleic acid sequencing was carried out on the encapsidated RNA-1-Int-GAD seen in lane 2 in panel c, and this revealed that the encapsidated RNA has preserved the GAD mutation and has not reverted to wild-type GDD. Duplicate sequencing chromatograms are aligned to the wild-type sequence encoding GDD to highlight the point mutation, with the relevant amino acids indicated above. Sequencing was carried out by Eurofins Scientific, and sequence alignment was carried out using Vector NTI Advance 11.5.3.

    Techniques Used: Purification, Construct, SDS Page, Staining, Agarose Gel Electrophoresis, Sequencing, Mutagenesis, Plasmid Preparation

    Heterologous RNA can be encapsidated when bordered by RNA-2 UTRs. (a) Expression of GFP following agroinfiltration of N. benthamiana leaves with the constructs indicated. GFP fluorescence was visualized under UV light at 7 dpi, with the empty pEAQ vector (e.v.) agroinfiltrated as a negative control. (b) RNA extracted from particles purified from plants agroinfiltrated with pEAQ-HT-VP60-24K together with GFP constructs flanked by different 5′ UTRs, as indicated, in the presence or absence of pBinPS1NT. In each case, RNA was extracted from 1.5 mg purified particles, and the resulting RNA was analyzed by denaturing agarose gel electrophoresis and subsequent Northern blotting. (Top left) Northern blotting using a probe specific for the coding region of GFP; (top right) agarose gel before transfer to nylon membranes stained with ethidium bromide; (bottom) Instant Blue-stained SDS-PAGE gel used to reveal processing of VP60 and protein content of the particle preparations. (c) Sequence analysis of the RNA-2 5′ UTR at the positions of the HT mutations. Sequencing was performed on HT -GFP RNA shown in lane 2 in panel b, from particles from leaves coinfiltrated with pBinPS1NT, pEAQ-HT-VP60-24K, and pEAQ-HT-GFP. The duplicate chromatograms show that the HT mutations have not reverted to the wild type prior to encapsidation and are still HT .
    Figure Legend Snippet: Heterologous RNA can be encapsidated when bordered by RNA-2 UTRs. (a) Expression of GFP following agroinfiltration of N. benthamiana leaves with the constructs indicated. GFP fluorescence was visualized under UV light at 7 dpi, with the empty pEAQ vector (e.v.) agroinfiltrated as a negative control. (b) RNA extracted from particles purified from plants agroinfiltrated with pEAQ-HT-VP60-24K together with GFP constructs flanked by different 5′ UTRs, as indicated, in the presence or absence of pBinPS1NT. In each case, RNA was extracted from 1.5 mg purified particles, and the resulting RNA was analyzed by denaturing agarose gel electrophoresis and subsequent Northern blotting. (Top left) Northern blotting using a probe specific for the coding region of GFP; (top right) agarose gel before transfer to nylon membranes stained with ethidium bromide; (bottom) Instant Blue-stained SDS-PAGE gel used to reveal processing of VP60 and protein content of the particle preparations. (c) Sequence analysis of the RNA-2 5′ UTR at the positions of the HT mutations. Sequencing was performed on HT -GFP RNA shown in lane 2 in panel b, from particles from leaves coinfiltrated with pBinPS1NT, pEAQ-HT-VP60-24K, and pEAQ-HT-GFP. The duplicate chromatograms show that the HT mutations have not reverted to the wild type prior to encapsidation and are still HT .

    Techniques Used: Expressing, Construct, Fluorescence, Plasmid Preparation, Negative Control, Purification, Agarose Gel Electrophoresis, Northern Blot, Staining, SDS Page, Sequencing

    RNA-2 is abundant in the cell even in the absence of RNA-1. (Top) Northern blot of total RNA extracted from agroinfiltrated leaf material probed with an RNA probe specific for RNA-2 positive strands. Leaves were either agroinfiltrated with pEAQ-RNA-2 alone or coinfiltrated with both pBinPS1NT and pEAQ-RNA-2 and were harvested at 1, 4, and 5 days postinfiltration (dpi). (Bottom) Ethidium bromide-stained denaturing agarose gel prior to transfer of the RNAs to the membrane, showing the levels of 25S rRNA present in each sample as a loading control.
    Figure Legend Snippet: RNA-2 is abundant in the cell even in the absence of RNA-1. (Top) Northern blot of total RNA extracted from agroinfiltrated leaf material probed with an RNA probe specific for RNA-2 positive strands. Leaves were either agroinfiltrated with pEAQ-RNA-2 alone or coinfiltrated with both pBinPS1NT and pEAQ-RNA-2 and were harvested at 1, 4, and 5 days postinfiltration (dpi). (Bottom) Ethidium bromide-stained denaturing agarose gel prior to transfer of the RNAs to the membrane, showing the levels of 25S rRNA present in each sample as a loading control.

    Techniques Used: Northern Blot, Staining, Agarose Gel Electrophoresis

    The 87K GAD mutation reduces replication efficiency, while the AAA mutation abolishes it. Total RNA was extracted from leaves agroinfiltrated with pEAQ-RNA-2 and an RNA-1-based construct, as indicated. Gene-specific qRT-PCR was carried out to quantify negative (-ve)-stranded RNA-1 and RNA-2 (replication intermediates) in the different samples. Data from three replicate experiments were analyzed using Bio-Rad CFX software to show normalized expression of negative-stranded RNA-1 (left) and RNA-2 (right) relative to RNA-1-32E. Error bars represent standard errors of the means.
    Figure Legend Snippet: The 87K GAD mutation reduces replication efficiency, while the AAA mutation abolishes it. Total RNA was extracted from leaves agroinfiltrated with pEAQ-RNA-2 and an RNA-1-based construct, as indicated. Gene-specific qRT-PCR was carried out to quantify negative (-ve)-stranded RNA-1 and RNA-2 (replication intermediates) in the different samples. Data from three replicate experiments were analyzed using Bio-Rad CFX software to show normalized expression of negative-stranded RNA-1 (left) and RNA-2 (right) relative to RNA-1-32E. Error bars represent standard errors of the means.

    Techniques Used: Mutagenesis, Construct, Quantitative RT-PCR, Software, Expressing

    Truncated RNA-2 constructs can be encapsidated in the presence of RNA-1. (a) Northern blots of RNA packaged in particles produced with different versions of RNA-2 with and without RNA-1. RNA was extracted from particles purified from leaves agroinfiltrated with HT -VP60-24K and an RNA-2 construct, as indicated, in the presence or absence of pBinPS1NT. In each case, the RNA was extracted from 3 mg purified particles, and the resulting RNA was split equally on two duplicate denaturing agarose gels for subsequent Northern blotting. (Left) Detection of RNA-1 (top) or RNA-2 (middle) with probes annealing to the 32K ProC sequence of RNA-1 or the RNA-2 5′ UTR, respectively; (right) denaturing agarose gels before transfer to nylon membranes; (bottom) purified particle preparations visualized on an Instant Blue-stained denaturing SDS-PAGE gel serving as a control for processing of VP60 and the use of equal amounts of particles for each RNA extraction. (b) HT -VP60 is encapsidated in the presence of RNA-1. The presence of encapsidated RNA was analyzed in purified particles extracted from plants transiently expressing pEAQ- HT -VP60-24K with or without pEAQ-XhoI-RNA-2 and with or without pBinPS1NT. RNA was extracted from 2 mg purified particles, and the resulting RNA was loaded onto a denaturing agarose gel for subsequent Northern blotting. (Left) Immunoblot detection of VP60 with the probe annealing to a sequence within the VP60 coding region that is partially removed in the construct resulting from XhoI digestion; (middle) denaturing agarose gel before transfer to a nylon membrane; (right) Instant Blue-stained protein on a denaturing SDS-PAGE gel serving as a control for processing of the VP60 protein precursor and the use of equal amounts of particles in each RNA extraction.
    Figure Legend Snippet: Truncated RNA-2 constructs can be encapsidated in the presence of RNA-1. (a) Northern blots of RNA packaged in particles produced with different versions of RNA-2 with and without RNA-1. RNA was extracted from particles purified from leaves agroinfiltrated with HT -VP60-24K and an RNA-2 construct, as indicated, in the presence or absence of pBinPS1NT. In each case, the RNA was extracted from 3 mg purified particles, and the resulting RNA was split equally on two duplicate denaturing agarose gels for subsequent Northern blotting. (Left) Detection of RNA-1 (top) or RNA-2 (middle) with probes annealing to the 32K ProC sequence of RNA-1 or the RNA-2 5′ UTR, respectively; (right) denaturing agarose gels before transfer to nylon membranes; (bottom) purified particle preparations visualized on an Instant Blue-stained denaturing SDS-PAGE gel serving as a control for processing of VP60 and the use of equal amounts of particles for each RNA extraction. (b) HT -VP60 is encapsidated in the presence of RNA-1. The presence of encapsidated RNA was analyzed in purified particles extracted from plants transiently expressing pEAQ- HT -VP60-24K with or without pEAQ-XhoI-RNA-2 and with or without pBinPS1NT. RNA was extracted from 2 mg purified particles, and the resulting RNA was loaded onto a denaturing agarose gel for subsequent Northern blotting. (Left) Immunoblot detection of VP60 with the probe annealing to a sequence within the VP60 coding region that is partially removed in the construct resulting from XhoI digestion; (middle) denaturing agarose gel before transfer to a nylon membrane; (right) Instant Blue-stained protein on a denaturing SDS-PAGE gel serving as a control for processing of the VP60 protein precursor and the use of equal amounts of particles in each RNA extraction.

    Techniques Used: Construct, Northern Blot, Produced, Purification, Sequencing, Staining, SDS Page, RNA Extraction, Expressing, Agarose Gel Electrophoresis

    28) Product Images from "Proteomic analysis of Biomphalaria glabrata plasma proteins with binding affinity to those expressed by early developing larval Schistosoma mansoni"

    Article Title: Proteomic analysis of Biomphalaria glabrata plasma proteins with binding affinity to those expressed by early developing larval Schistosoma mansoni

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1006081

    PCR amplification of NMRI and BS-90 B . glabrata galectin-related protein (GREP) transcripts. Complementary DNA synthesized from whole body RNA extracts of 10 individual NMRI and 10 BS-90 B . glabrata snails were used to generate amplification products of the near-complete coding region of the BS-90 GREP sequence. GREP amplicons for each snail sample (1–10) are shown. Primers to B . glabrata α-actinin served as a loading control. Note that GREP amplicons were generated using cDNA from all BS-90 samples tested, while only 4/10 NMRI snails produced amplicons, demonstrating differential GREP gene expression in the NMRI snail population.
    Figure Legend Snippet: PCR amplification of NMRI and BS-90 B . glabrata galectin-related protein (GREP) transcripts. Complementary DNA synthesized from whole body RNA extracts of 10 individual NMRI and 10 BS-90 B . glabrata snails were used to generate amplification products of the near-complete coding region of the BS-90 GREP sequence. GREP amplicons for each snail sample (1–10) are shown. Primers to B . glabrata α-actinin served as a loading control. Note that GREP amplicons were generated using cDNA from all BS-90 samples tested, while only 4/10 NMRI snails produced amplicons, demonstrating differential GREP gene expression in the NMRI snail population.

    Techniques Used: Polymerase Chain Reaction, Amplification, Synthesized, Sequencing, Generated, Produced, Expressing

    PCR amplification of NMRI and BS-90 B . glabrata ADAM-TS, FREP12, and CREP2 transcripts. Whole body total RNA from 10 individual NMRI and 10 BS-90 B . glabrata snails were subjected to cDNA synthesis and used in PCR analysis of the ADAM-TS metalloproteinase, FREP12 and CREP2 transcript expression. Amplicons of the predicted size are shown for each snail sample (1–10). Primers to B . glabrata α-actinin served as a loading control.
    Figure Legend Snippet: PCR amplification of NMRI and BS-90 B . glabrata ADAM-TS, FREP12, and CREP2 transcripts. Whole body total RNA from 10 individual NMRI and 10 BS-90 B . glabrata snails were subjected to cDNA synthesis and used in PCR analysis of the ADAM-TS metalloproteinase, FREP12 and CREP2 transcript expression. Amplicons of the predicted size are shown for each snail sample (1–10). Primers to B . glabrata α-actinin served as a loading control.

    Techniques Used: Polymerase Chain Reaction, Amplification, Expressing

    29) Product Images from "Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data"

    Article Title: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

    Journal: Genome Biology

    doi: 10.1186/s13059-018-1408-2

    Effect of conversion artefacts on the biases in WGBS. a Presence of unconverted cytosines as percentage of total cytosine content, measured by LC-MS for three different BS-conversion protocols. The three protocols differ by denaturation method (Heat or Alkaline) or molarity of bisulfite (4.5 vs 9 M for Am-BS) but not by BS incubation temperature (65–70 °C). Averaged fold differences in quantity are shown above horizontal brackets , and a dotted line shows the usual level of genomic 5mC for reference of scale. For conversion differences between methods with 50 and 65 °C incubation temperatures, see Additional file 2 : Figure S10a. b A theoretical sum of 5mC and unconverted C as measured by LC-MS for J1 WT mESCs for three BS conversion protocols. Both 5mC and unconverted C will be interpreted as 5mC after amplification of WGBS libraries, boosting the overall levels of methylation, depending on the BS treatment protocol. c Absolute quantification of unconverted cytosines in the unmethylated TKO mESC line, as measured by Heat and Alkaline BS-seq. d Context distribution of BS conversion artefacts; the value is the same for Heat and Alkaline and therefore plotted as an average. e CH methylation on both strands of the mouse major satellite repeat as measured by pre- and post-bisulfite WGBS methods. 5mC percentage from the BS cloning from Additional file 2 : Figure S5a is plotted in both panels for reference. Positive y-axis values indicate the top strand and negative the bottom strand. Statistical analyses in a – c were performed for matched experimental pairs with unpaired two-tailed t -tests against Heat in a and c , and WT ES in b . Error bars in a – c represent standard error of the mean, * p
    Figure Legend Snippet: Effect of conversion artefacts on the biases in WGBS. a Presence of unconverted cytosines as percentage of total cytosine content, measured by LC-MS for three different BS-conversion protocols. The three protocols differ by denaturation method (Heat or Alkaline) or molarity of bisulfite (4.5 vs 9 M for Am-BS) but not by BS incubation temperature (65–70 °C). Averaged fold differences in quantity are shown above horizontal brackets , and a dotted line shows the usual level of genomic 5mC for reference of scale. For conversion differences between methods with 50 and 65 °C incubation temperatures, see Additional file 2 : Figure S10a. b A theoretical sum of 5mC and unconverted C as measured by LC-MS for J1 WT mESCs for three BS conversion protocols. Both 5mC and unconverted C will be interpreted as 5mC after amplification of WGBS libraries, boosting the overall levels of methylation, depending on the BS treatment protocol. c Absolute quantification of unconverted cytosines in the unmethylated TKO mESC line, as measured by Heat and Alkaline BS-seq. d Context distribution of BS conversion artefacts; the value is the same for Heat and Alkaline and therefore plotted as an average. e CH methylation on both strands of the mouse major satellite repeat as measured by pre- and post-bisulfite WGBS methods. 5mC percentage from the BS cloning from Additional file 2 : Figure S5a is plotted in both panels for reference. Positive y-axis values indicate the top strand and negative the bottom strand. Statistical analyses in a – c were performed for matched experimental pairs with unpaired two-tailed t -tests against Heat in a and c , and WT ES in b . Error bars in a – c represent standard error of the mean, * p

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Incubation, Amplification, Methylation, Clone Assay, Two Tailed Test

    30) Product Images from "Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data"

    Article Title: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

    Journal: Genome Biology

    doi: 10.1186/s13059-018-1408-2

    Effect of DNA methylation status on the degradation and amplification biases. a Coverage of dinucleotides in WGBS datasets from unmethylated and in vitro M.CviPI-methylated TKO DNA prepared with the Heat BS-seq protocol. For direct comparison, the increase in coverage is expressed as fold difference from the genomic average and normalised to the AA dinucleotide. The dinucleotides are grouped as derived from C, G or A/T only and presented in the box-plot panel (right) as total percentage increase in coverage; crosses mark mean values and error bars represent minimum and maximum values. Statistical analysis was performed with one-way ANOVA with Dunnett’s multiple comparisons test against the AT-only dinucleotides; **** p
    Figure Legend Snippet: Effect of DNA methylation status on the degradation and amplification biases. a Coverage of dinucleotides in WGBS datasets from unmethylated and in vitro M.CviPI-methylated TKO DNA prepared with the Heat BS-seq protocol. For direct comparison, the increase in coverage is expressed as fold difference from the genomic average and normalised to the AA dinucleotide. The dinucleotides are grouped as derived from C, G or A/T only and presented in the box-plot panel (right) as total percentage increase in coverage; crosses mark mean values and error bars represent minimum and maximum values. Statistical analysis was performed with one-way ANOVA with Dunnett’s multiple comparisons test against the AT-only dinucleotides; **** p

    Techniques Used: DNA Methylation Assay, Amplification, In Vitro, Methylation, Derivative Assay

    31) Product Images from "Blockade of voltage-gated sodium channels inhibits invasion of endocrine-resistant breast cancer cells"

    Article Title: Blockade of voltage-gated sodium channels inhibits invasion of endocrine-resistant breast cancer cells

    Journal: International Journal of Oncology

    doi: 10.3892/ijo.2015.3239

    VGSC knockdown by siRNA transfection. (A) pII cells were seeded into 12-well plates, allowed to attach overnight and then either transfected with a scrambled sequence (open bar) or SCN5A siRNA (solid bar). RNA was extracted from the cells, converted to cDNA and PCR amplified. Ct values were converted to ratios as described in Materials and methods. Histobars represent mean ± SEM of 3 independent determinations. * Significant difference from control with p=0.026. (B and C) Cells were seeded into a μ-dish 35mm, high and incubated at 37°C/5% CO 2 for 24 h, then transfected with scrambled sequence (B) or SCN5A siRNA (C). After 48 h, cells were fixed and stained with Na v 1.5 antibody (red), phallotoxin (green) or DAPI (blue).
    Figure Legend Snippet: VGSC knockdown by siRNA transfection. (A) pII cells were seeded into 12-well plates, allowed to attach overnight and then either transfected with a scrambled sequence (open bar) or SCN5A siRNA (solid bar). RNA was extracted from the cells, converted to cDNA and PCR amplified. Ct values were converted to ratios as described in Materials and methods. Histobars represent mean ± SEM of 3 independent determinations. * Significant difference from control with p=0.026. (B and C) Cells were seeded into a μ-dish 35mm, high and incubated at 37°C/5% CO 2 for 24 h, then transfected with scrambled sequence (B) or SCN5A siRNA (C). After 48 h, cells were fixed and stained with Na v 1.5 antibody (red), phallotoxin (green) or DAPI (blue).

    Techniques Used: Transfection, Sequencing, Polymerase Chain Reaction, Amplification, Incubation, Staining

    32) Product Images from "PCR-Based Molecular Diagnosis of Hepatitis Virus (HBV and HDV) in HCV Infected Patients and Their Biochemical Study"

    Article Title: PCR-Based Molecular Diagnosis of Hepatitis Virus (HBV and HDV) in HCV Infected Patients and Their Biochemical Study

    Journal: Journal of Pathogens

    doi: 10.1155/2016/3219793

    A representative 1.5% agarose gel of PCR products for the detection of HCV. Lane M: DNA marker, lane 1: positive control (227 bp), lane 2: negative control, and lanes 3 to 15: patients positive for HCV RNA.
    Figure Legend Snippet: A representative 1.5% agarose gel of PCR products for the detection of HCV. Lane M: DNA marker, lane 1: positive control (227 bp), lane 2: negative control, and lanes 3 to 15: patients positive for HCV RNA.

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

    33) Product Images from "Recent pattern of Co-infection amongst HIV seropositive individuals in tertiary care hospital, kolkata"

    Article Title: Recent pattern of Co-infection amongst HIV seropositive individuals in tertiary care hospital, kolkata

    Journal: Virology Journal

    doi: 10.1186/1743-422X-8-116

    Electrophoretic pattern of nested RT –PCR and phylogenetic tree of HCV RNA positive individuals. A: Agarose gel picture of nested RT- PCR amplified product of 5'NCR of HCV genome. Lane 1: MW (100 bp DNA ladder); lane 2: positive control; lane 3: negative control; lane 3, 4, 5, 7, 8, 9, 10, 11, 12, 13 depicts the positive sample numbered HIV35, HIV61, HIV88, HIV97, HIV153, HIV173, HIV 175, HIV 176, HIV177 and HIV 190 respectively. B: Phylogenetic analysis of hepatitis C virus 5' non coding region. Phylogenetic analysis of 5' non coding region (nt -240 to -60; 181 bp) sequences of 10 HCV samples of HIV seropositive individuals. The sequences for major subtype were selected from the GeneBank database for analysis. The accession Numbers of the reference sequences (with subtypes are as follows: AF011753 (1A), AJ132996 (1B), AY051292 (1C), af238485 (2a), af238486 (2b), L38330 (2c), AF046866 (3a), D49374 (3b), D16612 (3c), D16620 (3d), D16618 (3e), X91421 (3g), Y11604 (4a), Y13184 (5a), Y12083 (6a) and the samples are numbered as HIV following the reference number.
    Figure Legend Snippet: Electrophoretic pattern of nested RT –PCR and phylogenetic tree of HCV RNA positive individuals. A: Agarose gel picture of nested RT- PCR amplified product of 5'NCR of HCV genome. Lane 1: MW (100 bp DNA ladder); lane 2: positive control; lane 3: negative control; lane 3, 4, 5, 7, 8, 9, 10, 11, 12, 13 depicts the positive sample numbered HIV35, HIV61, HIV88, HIV97, HIV153, HIV173, HIV 175, HIV 176, HIV177 and HIV 190 respectively. B: Phylogenetic analysis of hepatitis C virus 5' non coding region. Phylogenetic analysis of 5' non coding region (nt -240 to -60; 181 bp) sequences of 10 HCV samples of HIV seropositive individuals. The sequences for major subtype were selected from the GeneBank database for analysis. The accession Numbers of the reference sequences (with subtypes are as follows: AF011753 (1A), AJ132996 (1B), AY051292 (1C), af238485 (2a), af238486 (2b), L38330 (2c), AF046866 (3a), D49374 (3b), D16612 (3c), D16620 (3d), D16618 (3e), X91421 (3g), Y11604 (4a), Y13184 (5a), Y12083 (6a) and the samples are numbered as HIV following the reference number.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Amplification, Positive Control, Negative Control

    34) Product Images from "Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites"

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites

    Journal: Parasites & Vectors

    doi: 10.1186/s13071-017-1975-1

    Determination of in vitro transcribed RNAs and VLPs by agarose gel electrophoresis. a Agarose gel electrophoresis of in vitro transcribed RNAs. The size of the in vitro transcribed RNAs were marked above each lane and compared with a RNA marker (Thermo Fisher). b RNase A and DNase I digestion of VLPs. Lane 1: PET-MS2 (RNase A); Lane 2: PET-MS2 (DNase I); Lane 3: PET-MS2 (RNase A + DNase I); Lane 4: PET-MS2; Lane 5: YFV VLP(RNase A); Lane 6: YFV VLP (DNase I); Lane 7: YFV VLP (RNase A + DNase I); Lane 8: YFV VLP; Lane 9: EEEV VLP (RNase A); Lane 10: EEEV VLP (DNase I); Lane 11: EEEV VLP (RNase A + DNase I); Lane 12: EEEV VLP. The size of VLPs are compared to a DNA marker (TaKaRa). The nucleic acids between 1,000–2,000 bp are resistant to both RNase A and DNase I due to their packaging in the internal section of the VLPs
    Figure Legend Snippet: Determination of in vitro transcribed RNAs and VLPs by agarose gel electrophoresis. a Agarose gel electrophoresis of in vitro transcribed RNAs. The size of the in vitro transcribed RNAs were marked above each lane and compared with a RNA marker (Thermo Fisher). b RNase A and DNase I digestion of VLPs. Lane 1: PET-MS2 (RNase A); Lane 2: PET-MS2 (DNase I); Lane 3: PET-MS2 (RNase A + DNase I); Lane 4: PET-MS2; Lane 5: YFV VLP(RNase A); Lane 6: YFV VLP (DNase I); Lane 7: YFV VLP (RNase A + DNase I); Lane 8: YFV VLP; Lane 9: EEEV VLP (RNase A); Lane 10: EEEV VLP (DNase I); Lane 11: EEEV VLP (RNase A + DNase I); Lane 12: EEEV VLP. The size of VLPs are compared to a DNA marker (TaKaRa). The nucleic acids between 1,000–2,000 bp are resistant to both RNase A and DNase I due to their packaging in the internal section of the VLPs

    Techniques Used: In Vitro, Agarose Gel Electrophoresis, Marker, Positron Emission Tomography

    Amplification of serially diluted VLPs by both RT-PCR and PCR. a The layout of the MBVs hybridization capture-chip. The probe P is the QC probe. The probe NC is the negative control probe. b Amplifications of serially diluted VLPs by both RT-PCR and PCR (both based on the GSPs of RT-PCR system A or B). The results showed that although DNase I did not completely digest DNA templates in high concentration VLPs, the extraction of low-concentration VLPs were only detected by RT-PCR and not by PCR, demonstrating that DNA templates had been diluted to sufficiently. c Principle of the CL imaging DNA hybridization method. Step 1 shows that capture probes are fixed to the aldehyde-chip surface. Step 2 shows that the denatured RT-PCR products are hybridized on the capture-chip. Steps 3–5 show the principle of CL detection. Biotin is incorporated into reverse strand in RT-PCR amplification. When HRP modified streptavidin is bound, CL signal becomes illuminant by the catalyzed substrates
    Figure Legend Snippet: Amplification of serially diluted VLPs by both RT-PCR and PCR. a The layout of the MBVs hybridization capture-chip. The probe P is the QC probe. The probe NC is the negative control probe. b Amplifications of serially diluted VLPs by both RT-PCR and PCR (both based on the GSPs of RT-PCR system A or B). The results showed that although DNase I did not completely digest DNA templates in high concentration VLPs, the extraction of low-concentration VLPs were only detected by RT-PCR and not by PCR, demonstrating that DNA templates had been diluted to sufficiently. c Principle of the CL imaging DNA hybridization method. Step 1 shows that capture probes are fixed to the aldehyde-chip surface. Step 2 shows that the denatured RT-PCR products are hybridized on the capture-chip. Steps 3–5 show the principle of CL detection. Biotin is incorporated into reverse strand in RT-PCR amplification. When HRP modified streptavidin is bound, CL signal becomes illuminant by the catalyzed substrates

    Techniques Used: Amplification, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Hybridization, Chromatin Immunoprecipitation, Negative Control, Concentration Assay, Imaging, DNA Hybridization, Modification

    35) Product Images from "First detection and molecular characterization of a DENV‐1/ DENV‐4 co‐infection during an epidemic in Rio de Janeiro, Brazil. First detection and molecular characterization of a DENV‐1/DENV‐4 co‐infection during an epidemic in Rio de Janeiro, Brazil"

    Article Title: First detection and molecular characterization of a DENV‐1/ DENV‐4 co‐infection during an epidemic in Rio de Janeiro, Brazil. First detection and molecular characterization of a DENV‐1/DENV‐4 co‐infection during an epidemic in Rio de Janeiro, Brazil

    Journal: Clinical Case Reports

    doi: 10.1002/ccr3.1750

    Electrophoresis analysis and amplification curve of DENV ‐1 and DENV ‐4 genome by RT ‐ PCR for detection and genomic sequencing. A, Products amplified by RT ‐ PCR (Lanciotti, 1992) for the confirmation of DENV ‐1 and DENV ‐4 isolated. Lanes: 1—molecular weight (100 bp); 2—original isolate with the mixture of all DENV ‐specific primers; 3—original isolate with the reaction mixture containing only the DENV ‐1 type ‐specific primer ( TS 1); 4—original isolate with the reaction mixture containing only the DENV ‐4 type‐specific primer ( TS 4); 6—first viral passage in cell culture with the mixture of all DENV ‐specific primers; 7—first viral passage with DENV ‐1 type‐specific primer ( TS 1); 8—first viral passage in cell culture with DENV ‐4 type‐specific primer ( TS 4 9—negative control ( DNA se/ RNA se free water); 10—mixture of positive controls ( DENV ‐1 to 4). B, RT ‐ PCR amplicons for sequencing from the original isolates and first passage. Lanes: 1—molecular weight (100 bp); 2 and 3—original isolate with primers D1‐2a/D1‐3b and D1‐3a/D1‐4b, respectively; 4 and 5—original isolate with primers D4‐3/D4‐6 and D4‐5/D4‐8, respectively; 6 and 7—first passage with primers D1‐2a/D1‐3b and D1‐3a/D1‐4b, respectively; 8 and 9—first passage with primers D4‐3/D4‐6 and D4‐5/D4‐8, respectively. C and D, DENV ‐1 and DENV ‐4 amplification curves in the original isolated, respectively. E and F, DENV ‐1 and DENV ‐4 amplification curves in the first passage, respectively
    Figure Legend Snippet: Electrophoresis analysis and amplification curve of DENV ‐1 and DENV ‐4 genome by RT ‐ PCR for detection and genomic sequencing. A, Products amplified by RT ‐ PCR (Lanciotti, 1992) for the confirmation of DENV ‐1 and DENV ‐4 isolated. Lanes: 1—molecular weight (100 bp); 2—original isolate with the mixture of all DENV ‐specific primers; 3—original isolate with the reaction mixture containing only the DENV ‐1 type ‐specific primer ( TS 1); 4—original isolate with the reaction mixture containing only the DENV ‐4 type‐specific primer ( TS 4); 6—first viral passage in cell culture with the mixture of all DENV ‐specific primers; 7—first viral passage with DENV ‐1 type‐specific primer ( TS 1); 8—first viral passage in cell culture with DENV ‐4 type‐specific primer ( TS 4 9—negative control ( DNA se/ RNA se free water); 10—mixture of positive controls ( DENV ‐1 to 4). B, RT ‐ PCR amplicons for sequencing from the original isolates and first passage. Lanes: 1—molecular weight (100 bp); 2 and 3—original isolate with primers D1‐2a/D1‐3b and D1‐3a/D1‐4b, respectively; 4 and 5—original isolate with primers D4‐3/D4‐6 and D4‐5/D4‐8, respectively; 6 and 7—first passage with primers D1‐2a/D1‐3b and D1‐3a/D1‐4b, respectively; 8 and 9—first passage with primers D4‐3/D4‐6 and D4‐5/D4‐8, respectively. C and D, DENV ‐1 and DENV ‐4 amplification curves in the original isolated, respectively. E and F, DENV ‐1 and DENV ‐4 amplification curves in the first passage, respectively

    Techniques Used: Electrophoresis, Amplification, Reverse Transcription Polymerase Chain Reaction, Genomic Sequencing, Isolation, Molecular Weight, Cell Culture, Negative Control, Sequencing

    36) Product Images from "Heat Shock Treatment Increases the Frequency of Loss of an Erythromycin Resistance-Encoding Transposable Element from the Chromosome of Lactobacillus crispatus CHCC3692"

    Article Title: Heat Shock Treatment Increases the Frequency of Loss of an Erythromycin Resistance-Encoding Transposable Element from the Chromosome of Lactobacillus crispatus CHCC3692

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.69.12.7173-7180.2003

    Growth curves of CHCC3692 Erm r and CHCC3692 Erm s in MRS broth in the presence (+) (20 μg/ml) or absence (−) of erythromycin (erm). Zero indicates the start of growth (1%) from an overnight culture of CHCC3692 in MRS broth.
    Figure Legend Snippet: Growth curves of CHCC3692 Erm r and CHCC3692 Erm s in MRS broth in the presence (+) (20 μg/ml) or absence (−) of erythromycin (erm). Zero indicates the start of growth (1%) from an overnight culture of CHCC3692 in MRS broth.

    Techniques Used:

    Detection of sequences homologous to the transposase gene in the CHCC3692 Erm s isolate (lanes 1, 3, and 5) and in the wild-type strain (lanes 2, 4, and 6). The Southern blot was probed with a 32 P-labeled 800-bp fragment of transposase. Lanes 1 and 2, genomic DNA digested with Eco RI; lanes 3 and 4, DNA digested with Eco RI and Pst I; lanes 5 and 6, DNA digested with Pst I. Size markers are shown on the left and are based on an Eco RI/ Hin dIII digest of the λ phage.
    Figure Legend Snippet: Detection of sequences homologous to the transposase gene in the CHCC3692 Erm s isolate (lanes 1, 3, and 5) and in the wild-type strain (lanes 2, 4, and 6). The Southern blot was probed with a 32 P-labeled 800-bp fragment of transposase. Lanes 1 and 2, genomic DNA digested with Eco RI; lanes 3 and 4, DNA digested with Eco RI and Pst I; lanes 5 and 6, DNA digested with Pst I. Size markers are shown on the left and are based on an Eco RI/ Hin dIII digest of the λ phage.

    Techniques Used: Southern Blot, Labeling

    Agarose gel electrophoresis of PCR-amplified DNA fragments from L. crispatus CHCC3692. Lanes 3 and 5 to 7, DNA amplified with transposase primers and templates derived from wild-type (Erm r ) and erythromycin-sensitive (Erm s ) isolates, respectively; lanes 9 and 10 to 12, DNA amplified with specific 16S Lactobacillus species primers and templates isolated from the Erm r and Erm s isolates, respectively. Lanes 5 and 10, template DNA was isolated from a spontaneous Erm s isolate; lanes 6 and 11, template DNA was derived from cells that were heat shocked at 60°C for 10 min; lanes 7 and 12, template DNA was isolated from cells that were heat shocked at 60°C for 20 min; lane 1, reference standard marker (λ DNA digested with Eco RI and Hin dIII).
    Figure Legend Snippet: Agarose gel electrophoresis of PCR-amplified DNA fragments from L. crispatus CHCC3692. Lanes 3 and 5 to 7, DNA amplified with transposase primers and templates derived from wild-type (Erm r ) and erythromycin-sensitive (Erm s ) isolates, respectively; lanes 9 and 10 to 12, DNA amplified with specific 16S Lactobacillus species primers and templates isolated from the Erm r and Erm s isolates, respectively. Lanes 5 and 10, template DNA was isolated from a spontaneous Erm s isolate; lanes 6 and 11, template DNA was derived from cells that were heat shocked at 60°C for 10 min; lanes 7 and 12, template DNA was isolated from cells that were heat shocked at 60°C for 20 min; lane 1, reference standard marker (λ DNA digested with Eco RI and Hin dIII).

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Derivative Assay, Isolation, Marker

    Schematic outline of the erm transposon, Tn 3692 , in L. crispatus CHCC3692. The upper part depicts the relative map of the transposon in the wild type (Erm r ), with restriction sites for the endonucleases Eco RI and Pst I. The lower part depicts the structure after removal of the erm transposable element. tps , transposase-encoding gene, tps ′, truncated transposase gene; erm (B), erythromycin resistance-encoding gene. The gray shaded box (130 nt) encodes an unknown protein. The arrows protruding from the tps genes indicate the direct repeats of the 50-nt fragment (not drawn to scale). The chromosomal structure in Erm s isolates is most likely a result of intragenic recombination between the direct repeats of the C-terminal transposase-encoding regions. The arrows indicate the direction of transcription. See text for further information.
    Figure Legend Snippet: Schematic outline of the erm transposon, Tn 3692 , in L. crispatus CHCC3692. The upper part depicts the relative map of the transposon in the wild type (Erm r ), with restriction sites for the endonucleases Eco RI and Pst I. The lower part depicts the structure after removal of the erm transposable element. tps , transposase-encoding gene, tps ′, truncated transposase gene; erm (B), erythromycin resistance-encoding gene. The gray shaded box (130 nt) encodes an unknown protein. The arrows protruding from the tps genes indicate the direct repeats of the 50-nt fragment (not drawn to scale). The chromosomal structure in Erm s isolates is most likely a result of intragenic recombination between the direct repeats of the C-terminal transposase-encoding regions. The arrows indicate the direction of transcription. See text for further information.

    Techniques Used:

    Agarose gel electrophoresis of PCR-amplified DNA fragments from L. crispatus CHCC3692. Lane 2, amplified DNA from the wild type (Erm r ); lanes 3 to 5, amplified DNA fragments from Erm s isolates undergoing 0, 10, and 20 min of heat shock at 60°C, respectively; lane 1, reference standard marker based on an Eco RI/ Hin dIII digest of phage λ.
    Figure Legend Snippet: Agarose gel electrophoresis of PCR-amplified DNA fragments from L. crispatus CHCC3692. Lane 2, amplified DNA from the wild type (Erm r ); lanes 3 to 5, amplified DNA fragments from Erm s isolates undergoing 0, 10, and 20 min of heat shock at 60°C, respectively; lane 1, reference standard marker based on an Eco RI/ Hin dIII digest of phage λ.

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Marker

    37) Product Images from "Site-Specific Integration of Transgenes in Soybean via Recombinase-Mediated DNA Cassette Exchange [OA]"

    Article Title: Site-Specific Integration of Transgenes in Soybean via Recombinase-Mediated DNA Cassette Exchange [OA]

    Journal: Plant Physiology

    doi: 10.1104/pp.109.137612

    Southern hybridization analysis of RMCE T0 and T1 plants. Genomic DNA was digested with Nde I and hybridized sequentially with probes hpt (A), scp1 (B), ubq (C), and flp (D). Target-specific bands “t,” hybridizing to both the scp1 and hpt probes, were detected in target homozygous plants A, B, and C. RMCE-specific bands “r1” for hemizygous and “r2” for homozygous samples, hybridizing to both the scp1 and ubq probes, were detected in RMCE-excision T0 plants A2-3, A2-4, B5-1, and B5-2, RMCE-RMCE T0 plants C3-1 and C3-2, RMCE-excision T1 plants A2-3-1 and A2-3-1, and RMCE-RMCE T1 plants B5-1-1, B5-2-1, C3-1-1, and C3-1-2. The RMCE-specific bands are 3,276 bp larger than the corresponding target-specific bands. Excision-specific bands “e1” for hemizygous and “e2” for homozygous samples, hybridizing to only the scp1 probe, were detected in RMCE-excision T0 plants A2-3 and A2-4, RMCE-excision T1 plants A2-3-1 and A2-3-2, and excision-excision T1 plants A2-3-3 and A2-3-4. The ubq probe hybridized to an approximately 6-kb wild-type band “w” in all samples. Donor-specific bands “d,” hybridizing to only the ubq probe, were detected in as many as five copies in RMCE-excision T0 plants A2-3 and A2-4, one copy in RMCE-excision T1 plants A2-3-1 and A2-3-2, and two copies in excision-excision T1 plants A2-3-3 and A2-3-4. The top ubq bands “d-f” of RMCE-RMCE T0 plants C3-1 and C3-2 were also hybridized by the scp1 probe. They might represent mingled flp DNA QC292 containing the scp1 promoter and the donor DNA QC329 containing the ubq gene. flp -specific bands “f,” hybridizing to both the flp and scp1 probes, were detected in RMCE-excision T0 plants A2-3 and A2-4. The DIGVII markers are 8,576, 7,427, 6,106, 4,899, 3,639, 2,799, 1,953, and 1,882 bp. Only the first band of a group of bands is marked.
    Figure Legend Snippet: Southern hybridization analysis of RMCE T0 and T1 plants. Genomic DNA was digested with Nde I and hybridized sequentially with probes hpt (A), scp1 (B), ubq (C), and flp (D). Target-specific bands “t,” hybridizing to both the scp1 and hpt probes, were detected in target homozygous plants A, B, and C. RMCE-specific bands “r1” for hemizygous and “r2” for homozygous samples, hybridizing to both the scp1 and ubq probes, were detected in RMCE-excision T0 plants A2-3, A2-4, B5-1, and B5-2, RMCE-RMCE T0 plants C3-1 and C3-2, RMCE-excision T1 plants A2-3-1 and A2-3-1, and RMCE-RMCE T1 plants B5-1-1, B5-2-1, C3-1-1, and C3-1-2. The RMCE-specific bands are 3,276 bp larger than the corresponding target-specific bands. Excision-specific bands “e1” for hemizygous and “e2” for homozygous samples, hybridizing to only the scp1 probe, were detected in RMCE-excision T0 plants A2-3 and A2-4, RMCE-excision T1 plants A2-3-1 and A2-3-2, and excision-excision T1 plants A2-3-3 and A2-3-4. The ubq probe hybridized to an approximately 6-kb wild-type band “w” in all samples. Donor-specific bands “d,” hybridizing to only the ubq probe, were detected in as many as five copies in RMCE-excision T0 plants A2-3 and A2-4, one copy in RMCE-excision T1 plants A2-3-1 and A2-3-2, and two copies in excision-excision T1 plants A2-3-3 and A2-3-4. The top ubq bands “d-f” of RMCE-RMCE T0 plants C3-1 and C3-2 were also hybridized by the scp1 probe. They might represent mingled flp DNA QC292 containing the scp1 promoter and the donor DNA QC329 containing the ubq gene. flp -specific bands “f,” hybridizing to both the flp and scp1 probes, were detected in RMCE-excision T0 plants A2-3 and A2-4. The DIGVII markers are 8,576, 7,427, 6,106, 4,899, 3,639, 2,799, 1,953, and 1,882 bp. Only the first band of a group of bands is marked.

    Techniques Used: Hybridization

    38) Product Images from "Oral Administration of a Select Mixture of Bacillus Probiotics Affects the Gut Microbiota and Goblet Cell Function following Escherichia coli Challenge in Newly Weaned Pigs of Genotype MUC4 That Are Supposed To Be Enterotoxigenic E. coli F4ab/ac Receptor Negative"

    Article Title: Oral Administration of a Select Mixture of Bacillus Probiotics Affects the Gut Microbiota and Goblet Cell Function following Escherichia coli Challenge in Newly Weaned Pigs of Genotype MUC4 That Are Supposed To Be Enterotoxigenic E. coli F4ab/ac Receptor Negative

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.02747-16

    16S rRNA gene sequencing.
    Figure Legend Snippet: 16S rRNA gene sequencing.

    Techniques Used: Sequencing

    39) Product Images from "Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq"

    Article Title: Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq

    Journal: RNA

    doi: 10.1261/rna.058115.116

    ( A ) A schematic representation of DO-RIP-seq procedure. (MNase, micrococcal nuclease; HuR DO-RIP, DO-RIP done with antibodies against HuR; NEG DO-RIP, negative control DO-RIP with nonspecific antibodies; PAGE, polyacrylamide gel electrophoresis.) ( B ) Optimization of MNase digestion using immunoprecipitated HuR RNPs. Various amounts of MNase (across the top : gel units of MNase/µg total RNA) were tested (nt, nucleotides). The green rectangle demarcates the preferred conditions; in this case between 73 and 18 gel units of MNase per µg total RNA. ( C ) RNA fragments after MNase digestion of cell lysates from three biological replicates of HuR (HuR.1/.2/.3) and negative control (Neg.1/.2/.3) DO-RIPs. The boxes demarcate the region of each gel from which RNA was extracted and used to prepare cDNA libraries for sequencing. ( D ) and DO-RIP-seq transcriptome coverage derived from cDNA libraries of immunoprecipitated HuR and Neg based on fragments per thousand per million (FPKM). ([NPC] negative control PAR-CLIP, [HPC] HuR PAR-CLIP, [NDR] negative control DO-RIP-seq, [HDR] HuR DO-RIP-seq). ( E ) Comparative matrix of R-correlation values for the number of aligned reads at 5-nt intervals of three replicates of HuR and Neg DO-RIP-seq libraries.
    Figure Legend Snippet: ( A ) A schematic representation of DO-RIP-seq procedure. (MNase, micrococcal nuclease; HuR DO-RIP, DO-RIP done with antibodies against HuR; NEG DO-RIP, negative control DO-RIP with nonspecific antibodies; PAGE, polyacrylamide gel electrophoresis.) ( B ) Optimization of MNase digestion using immunoprecipitated HuR RNPs. Various amounts of MNase (across the top : gel units of MNase/µg total RNA) were tested (nt, nucleotides). The green rectangle demarcates the preferred conditions; in this case between 73 and 18 gel units of MNase per µg total RNA. ( C ) RNA fragments after MNase digestion of cell lysates from three biological replicates of HuR (HuR.1/.2/.3) and negative control (Neg.1/.2/.3) DO-RIPs. The boxes demarcate the region of each gel from which RNA was extracted and used to prepare cDNA libraries for sequencing. ( D ) and DO-RIP-seq transcriptome coverage derived from cDNA libraries of immunoprecipitated HuR and Neg based on fragments per thousand per million (FPKM). ([NPC] negative control PAR-CLIP, [HPC] HuR PAR-CLIP, [NDR] negative control DO-RIP-seq, [HDR] HuR DO-RIP-seq). ( E ) Comparative matrix of R-correlation values for the number of aligned reads at 5-nt intervals of three replicates of HuR and Neg DO-RIP-seq libraries.

    Techniques Used: Negative Control, Polyacrylamide Gel Electrophoresis, Immunoprecipitation, Sequencing, Derivative Assay, Cross-linking Immunoprecipitation

    ( A ) HuR DO-RIP-seq binding site (red bar and shading) in the CCND1 ). The log of odds score (LOD) and read depth in reads per million (RPM) are depicted. ( B ) A comparison of the abundance of HuR binding sites in locations across the transcriptome ([3′UTR] 3′ untranslated region, [5′UTR] 5′ untranslated region, [CDS] coding sequence exons, [ncRNA] noncoding RNA). ( C ) Sequence logo of the most frequently observed cDNA nonamer in HuR binding sites. ( D ) CDF plot comparing log 2 fold-change in mRNA expression following HuR siRNA knockdown for HuR targets identified by DO-RIP-seq, PAR-CLIP, both, or neither. A rightward . ( E ) HuR binding site saturation analysis. The fractions of significantly enriched ( P -value
    Figure Legend Snippet: ( A ) HuR DO-RIP-seq binding site (red bar and shading) in the CCND1 ). The log of odds score (LOD) and read depth in reads per million (RPM) are depicted. ( B ) A comparison of the abundance of HuR binding sites in locations across the transcriptome ([3′UTR] 3′ untranslated region, [5′UTR] 5′ untranslated region, [CDS] coding sequence exons, [ncRNA] noncoding RNA). ( C ) Sequence logo of the most frequently observed cDNA nonamer in HuR binding sites. ( D ) CDF plot comparing log 2 fold-change in mRNA expression following HuR siRNA knockdown for HuR targets identified by DO-RIP-seq, PAR-CLIP, both, or neither. A rightward . ( E ) HuR binding site saturation analysis. The fractions of significantly enriched ( P -value

    Techniques Used: Binding Assay, Sequencing, Expressing, Cross-linking Immunoprecipitation

    40) Product Images from "RNA Contaminates Glycosaminoglycans Extracted from Cells and Tissues"

    Article Title: RNA Contaminates Glycosaminoglycans Extracted from Cells and Tissues

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0167336

    Schematic workflow for glycosaminoglycan (GAG) extraction including RNase treatment Cell/tissue lysates are treated overnight with proteinase K (Prot. K), followed by DNase-I and RNase-I treatment and finally chloroform extraction and dialysis to remove contaminating proteins/DNA/RNA. After drying/concentration of GAG extracts, the purity of the preparations is assessed using ethidium bromide (EtBr) agarose gel electrophoresis, or by measuring the absorbance at 260 nm (A260).
    Figure Legend Snippet: Schematic workflow for glycosaminoglycan (GAG) extraction including RNase treatment Cell/tissue lysates are treated overnight with proteinase K (Prot. K), followed by DNase-I and RNase-I treatment and finally chloroform extraction and dialysis to remove contaminating proteins/DNA/RNA. After drying/concentration of GAG extracts, the purity of the preparations is assessed using ethidium bromide (EtBr) agarose gel electrophoresis, or by measuring the absorbance at 260 nm (A260).

    Techniques Used: Concentration Assay, Agarose Gel Electrophoresis

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    Article Snippet: .. The programme ended with an extension step at 72°C for 10 min. Amplified products were examined by agarose gel electrophoresis (1%), purified using a QIAquick Gel Extraction kit (QIAGEN, Germany), and then sequenced directly. .. Sequencing of the 5′ UTR and 3′ UTR were determined by using 5′ RACE and 3′ RACE system for Rapid Amplification of cDNA Ends (Invitrogen) respectively.

    Article Title: Recombining overlapping BACs into a single larger BAC
    Article Snippet: .. For recombination with pBACLinkSpAB and pBACLinkGmBC, Not I linearized DNA was gel purified using the Qiaquick Gel Extraction Kit (Qiagen). .. After electroporation as described above, the bacteria were spread on plates containing 50 μg/ml of spectinomycin or 5 μg/ml gentamycin respectively.

    Article Title: Utility of arsenic-treated bird skins for DNA extraction
    Article Snippet: .. All 600 bp PCR fragments were purified from agarose gels using the Qiaquick Gel Extraction Kit (Qiagen) and cloned (TOPO TA Cloning Kit, Invitrogen) prior to sequencing. .. Sequencing of cloned PCR products (both strands) was performed with universal M13 primers by AGOWA.

    Article Title: Optimized design of antisense oligomers for targeted rRNA depletion
    Article Snippet: .. Initial samples for the X. laevis 28S qRT-PCR were column purified (Qiagen #28704) and used at full concentration for qRT-PCR; subsequent samples were used directly at 1:10 dilution for qRT-PCR based on the results of a 4-sample, 1:5 dilution calibration curve analysis. qRT-PCR was performed in triplicate using 10μl reactions (2.5μl of cDNA, 5 μM of each forward and reverse primers, and 2x SYGreen mix (Genesee #17-505B)). qPCR was performed on QuantStudio 3 (Applied Biosystems) with an initial heat activation at 50°C for 2 minutes and then 95°C for 10 minutes. ..

    Article Title: High Prevalence of Hepatitis C Virus Genotype 1b Infection in a Small Town of Argentina. Phylogenetic and Bayesian Coalescent Analysis
    Article Snippet: .. The amplified DNAs were purified from agarose gels using a commercial kit (QIAquik Gel Extraction Kit protocol, QIAGEN) and the amplicons were sequenced in both senses using the internal PCR primers. ..

    Article Title: A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain
    Article Snippet: .. The P1316 plasmid was also NotI/AscI digested and gel purified (Qiagen/QiaQuick Gel Extraction Cat# 28706). .. P1316 is a derivative of the pTT3 expression vector ( ) and consists of (5’ to 3’): a CMV promoter, the mouse V kappa leader sequence, a NotI restriction site, an insert consisting of VL /joining fragment/VH , and the mouse IgG1 CH sequence amplified from mouse genomic DNA, flanked by AscI and XbaI restriction sites ( ; ).

    Real-time Polymerase Chain Reaction:

    Article Title: Optimized design of antisense oligomers for targeted rRNA depletion
    Article Snippet: .. Initial samples for the X. laevis 28S qRT-PCR were column purified (Qiagen #28704) and used at full concentration for qRT-PCR; subsequent samples were used directly at 1:10 dilution for qRT-PCR based on the results of a 4-sample, 1:5 dilution calibration curve analysis. qRT-PCR was performed in triplicate using 10μl reactions (2.5μl of cDNA, 5 μM of each forward and reverse primers, and 2x SYGreen mix (Genesee #17-505B)). qPCR was performed on QuantStudio 3 (Applied Biosystems) with an initial heat activation at 50°C for 2 minutes and then 95°C for 10 minutes. ..

    Concentration Assay:

    Article Title: Optimized design of antisense oligomers for targeted rRNA depletion
    Article Snippet: .. Initial samples for the X. laevis 28S qRT-PCR were column purified (Qiagen #28704) and used at full concentration for qRT-PCR; subsequent samples were used directly at 1:10 dilution for qRT-PCR based on the results of a 4-sample, 1:5 dilution calibration curve analysis. qRT-PCR was performed in triplicate using 10μl reactions (2.5μl of cDNA, 5 μM of each forward and reverse primers, and 2x SYGreen mix (Genesee #17-505B)). qPCR was performed on QuantStudio 3 (Applied Biosystems) with an initial heat activation at 50°C for 2 minutes and then 95°C for 10 minutes. ..

    Polymerase Chain Reaction:

    Article Title: Gene Constellation of Influenza A Virus Reassortants with High Growth Phenotype Prepared as Seed Candidates for Vaccine Production
    Article Snippet: .. DNA purification PCR products were gel purified in a 2% low melt agarose gel using QIAquick® Gel Extraction Kit (Qiagen Inc., Valencia, CA) per manufacturer's recommendations. .. The extracted PCR products were visualized for purity on a 2% agarose-TAE/EtBr gel.

    Article Title: Fluorescence-based methods for measuring target interference by CRISPR-Cas systems
    Article Snippet: .. T4 polynucleotide kinase (PNK), NotI, NcoI, T4 DNA ligase and accompanying buffers purchased from New England Biolabs 100 mM ATP 100 µM CRISPR target oligonucleotides (designed as in ) and pACYC-GFP Gel purification kit (e.g. Qiagen QIAquick Gel Extraction kit or Promega Wizard SV Gel and PCR Clean-Up System) One Shot TOP10 Competent Cells (Thermo-Fisher) or similar cloning E. coli strain Miniprep kit (Qiagen or Promega) ..

    Article Title: Utility of arsenic-treated bird skins for DNA extraction
    Article Snippet: .. All 600 bp PCR fragments were purified from agarose gels using the Qiaquick Gel Extraction Kit (Qiagen) and cloned (TOPO TA Cloning Kit, Invitrogen) prior to sequencing. .. Sequencing of cloned PCR products (both strands) was performed with universal M13 primers by AGOWA.

    Article Title: High Prevalence of Hepatitis C Virus Genotype 1b Infection in a Small Town of Argentina. Phylogenetic and Bayesian Coalescent Analysis
    Article Snippet: .. The amplified DNAs were purified from agarose gels using a commercial kit (QIAquik Gel Extraction Kit protocol, QIAGEN) and the amplicons were sequenced in both senses using the internal PCR primers. ..

    DNA Purification:

    Article Title: Gene Constellation of Influenza A Virus Reassortants with High Growth Phenotype Prepared as Seed Candidates for Vaccine Production
    Article Snippet: .. DNA purification PCR products were gel purified in a 2% low melt agarose gel using QIAquick® Gel Extraction Kit (Qiagen Inc., Valencia, CA) per manufacturer's recommendations. .. The extracted PCR products were visualized for purity on a 2% agarose-TAE/EtBr gel.

    CRISPR:

    Article Title: Fluorescence-based methods for measuring target interference by CRISPR-Cas systems
    Article Snippet: .. T4 polynucleotide kinase (PNK), NotI, NcoI, T4 DNA ligase and accompanying buffers purchased from New England Biolabs 100 mM ATP 100 µM CRISPR target oligonucleotides (designed as in ) and pACYC-GFP Gel purification kit (e.g. Qiagen QIAquick Gel Extraction kit or Promega Wizard SV Gel and PCR Clean-Up System) One Shot TOP10 Competent Cells (Thermo-Fisher) or similar cloning E. coli strain Miniprep kit (Qiagen or Promega) ..

    Sequencing:

    Article Title: Utility of arsenic-treated bird skins for DNA extraction
    Article Snippet: .. All 600 bp PCR fragments were purified from agarose gels using the Qiaquick Gel Extraction Kit (Qiagen) and cloned (TOPO TA Cloning Kit, Invitrogen) prior to sequencing. .. Sequencing of cloned PCR products (both strands) was performed with universal M13 primers by AGOWA.

    Gel Extraction:

    Article Title: Gene Constellation of Influenza A Virus Reassortants with High Growth Phenotype Prepared as Seed Candidates for Vaccine Production
    Article Snippet: .. DNA purification PCR products were gel purified in a 2% low melt agarose gel using QIAquick® Gel Extraction Kit (Qiagen Inc., Valencia, CA) per manufacturer's recommendations. .. The extracted PCR products were visualized for purity on a 2% agarose-TAE/EtBr gel.

    Article Title: Genotype V Japanese Encephalitis Virus Is Emerging
    Article Snippet: .. The programme ended with an extension step at 72°C for 10 min. Amplified products were examined by agarose gel electrophoresis (1%), purified using a QIAquick Gel Extraction kit (QIAGEN, Germany), and then sequenced directly. .. Sequencing of the 5′ UTR and 3′ UTR were determined by using 5′ RACE and 3′ RACE system for Rapid Amplification of cDNA Ends (Invitrogen) respectively.

    Article Title: Fluorescence-based methods for measuring target interference by CRISPR-Cas systems
    Article Snippet: .. T4 polynucleotide kinase (PNK), NotI, NcoI, T4 DNA ligase and accompanying buffers purchased from New England Biolabs 100 mM ATP 100 µM CRISPR target oligonucleotides (designed as in ) and pACYC-GFP Gel purification kit (e.g. Qiagen QIAquick Gel Extraction kit or Promega Wizard SV Gel and PCR Clean-Up System) One Shot TOP10 Competent Cells (Thermo-Fisher) or similar cloning E. coli strain Miniprep kit (Qiagen or Promega) ..

    Article Title: Recombining overlapping BACs into a single larger BAC
    Article Snippet: .. For recombination with pBACLinkSpAB and pBACLinkGmBC, Not I linearized DNA was gel purified using the Qiaquick Gel Extraction Kit (Qiagen). .. After electroporation as described above, the bacteria were spread on plates containing 50 μg/ml of spectinomycin or 5 μg/ml gentamycin respectively.

    Article Title: Utility of arsenic-treated bird skins for DNA extraction
    Article Snippet: .. All 600 bp PCR fragments were purified from agarose gels using the Qiaquick Gel Extraction Kit (Qiagen) and cloned (TOPO TA Cloning Kit, Invitrogen) prior to sequencing. .. Sequencing of cloned PCR products (both strands) was performed with universal M13 primers by AGOWA.

    Article Title: High Prevalence of Hepatitis C Virus Genotype 1b Infection in a Small Town of Argentina. Phylogenetic and Bayesian Coalescent Analysis
    Article Snippet: .. The amplified DNAs were purified from agarose gels using a commercial kit (QIAquik Gel Extraction Kit protocol, QIAGEN) and the amplicons were sequenced in both senses using the internal PCR primers. ..

    Article Title: A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain
    Article Snippet: .. The P1316 plasmid was also NotI/AscI digested and gel purified (Qiagen/QiaQuick Gel Extraction Cat# 28706). .. P1316 is a derivative of the pTT3 expression vector ( ) and consists of (5’ to 3’): a CMV promoter, the mouse V kappa leader sequence, a NotI restriction site, an insert consisting of VL /joining fragment/VH , and the mouse IgG1 CH sequence amplified from mouse genomic DNA, flanked by AscI and XbaI restriction sites ( ; ).

    Plasmid Preparation:

    Article Title: A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain
    Article Snippet: .. The P1316 plasmid was also NotI/AscI digested and gel purified (Qiagen/QiaQuick Gel Extraction Cat# 28706). .. P1316 is a derivative of the pTT3 expression vector ( ) and consists of (5’ to 3’): a CMV promoter, the mouse V kappa leader sequence, a NotI restriction site, an insert consisting of VL /joining fragment/VH , and the mouse IgG1 CH sequence amplified from mouse genomic DNA, flanked by AscI and XbaI restriction sites ( ; ).

    Gel Purification:

    Article Title: Fluorescence-based methods for measuring target interference by CRISPR-Cas systems
    Article Snippet: .. T4 polynucleotide kinase (PNK), NotI, NcoI, T4 DNA ligase and accompanying buffers purchased from New England Biolabs 100 mM ATP 100 µM CRISPR target oligonucleotides (designed as in ) and pACYC-GFP Gel purification kit (e.g. Qiagen QIAquick Gel Extraction kit or Promega Wizard SV Gel and PCR Clean-Up System) One Shot TOP10 Competent Cells (Thermo-Fisher) or similar cloning E. coli strain Miniprep kit (Qiagen or Promega) ..

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    Qiagen agarose gel extraction protocol
    Agarose Gel Extraction Protocol, supplied by Qiagen, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agarose gel extraction protocol/product/Qiagen
    Average 85 stars, based on 1 article reviews
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    agarose gel extraction protocol - by Bioz Stars, 2020-09
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