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microarray hybridization solution version 2  (Danaher Inc)


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    Danaher Inc microarray hybridization solution version 2
    Microarray Hybridization Solution Version 2, supplied by Danaher Inc, used in various techniques. Bioz Stars score: 93/100, based on 116 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/microarray+solution/Microarray+Hybridization+Solution+v2%2E0/pmc01175033-123-5-10
    Average 93 stars, based on 116 article reviews
    microarray hybridization solution version 2 - by Bioz Stars, 2026-10
    93/100 stars

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    Related Articles

    Hybridization:

    Article Title: Expression and Functional Analysis of lncRNAs Involved in Platelet-Derived Growth Factor-BB-Induced Proliferation of Human Aortic Smooth Muscle Cells
    Article Snippet: Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000; 1 μg of each labeled cRNA was fragmented by adding 5 μL of 10 × Blocking Agent and 1 μL of 25 × Fragmentation Buffer and then heated at 60°C for 30 min. .. Finally, 25 μL of 2 × GE Hybridization Buffer was added to dilute the labeled cRNA; 50 μL of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. .. Slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

    Article Title: Characterization of histopathology and gene-expression profiles of synovitis in early rheumatoid arthritis using targeted biopsy specimens
    Article Snippet: The PCR products were spotted in duplicate on type VII glass slides (Amersham Biosciences) with a Microarray Spotter Generation III (Amersham Biosciences). .. Labeled probes were mixed with Microarray Hybridization Solution Version 2 (Amersham Biosciences) and formamide (Sigma Chemical Co, St Louis, MO, USA) to a final concentration of 50%. ..

    Article Title: A small number of male-biased candidate pheromone receptors are expressed in large subsets of the olfactory sensory neurons in the antennae of drones from the European honey bee Apis mellifera.
    Article Snippet: .. Each slide with tissue sections was covered with 130 μL hybridization solution 1 [50% formamide, 25% H2O, 25% Microarray hybridization solution version 2.0 (GE Healthcare, Freiburg, Germany)] supplemented with the labeled riboprobe. ..

    Article Title: The Sensilla-Specific Expression and Subcellular Localization of SNMP1 and SNMP2 Reveal Novel Insights into Their Roles in the Antenna of the Desert Locust Schistocerca gregaria
    Article Snippet: .. After sectioning, the samples were treated for 20 min at 4 °C with 4% paraformaldehyde dissolved in PBS, washed in PBS for 5 min, and then incubated in 0.2 M HCl for 10 min. After washing the samples two times for 2 min in PBS, the slides were transferred into pre-hybridization solution (5× SSC (0.75 M NaCl, 0.075 M sodium citrate, pH 7.0) and 50% formamide) for 10 min. Next, each slide was covered with 130 μL hybridization solution (50% formamide, 25% H 2 O, 25% Microarray Hybridization Solution Version 2.0 (GE Healthcare, Freiburg, Germany)) containing either the ORCO or the SNMP1 antisense riboprobe. ..

    Labeling:

    Article Title: Expression and Functional Analysis of lncRNAs Involved in Platelet-Derived Growth Factor-BB-Induced Proliferation of Human Aortic Smooth Muscle Cells
    Article Snippet: Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000; 1 μg of each labeled cRNA was fragmented by adding 5 μL of 10 × Blocking Agent and 1 μL of 25 × Fragmentation Buffer and then heated at 60°C for 30 min. .. Finally, 25 μL of 2 × GE Hybridization Buffer was added to dilute the labeled cRNA; 50 μL of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. .. Slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

    Article Title: Characterization of histopathology and gene-expression profiles of synovitis in early rheumatoid arthritis using targeted biopsy specimens
    Article Snippet: The PCR products were spotted in duplicate on type VII glass slides (Amersham Biosciences) with a Microarray Spotter Generation III (Amersham Biosciences). .. Labeled probes were mixed with Microarray Hybridization Solution Version 2 (Amersham Biosciences) and formamide (Sigma Chemical Co, St Louis, MO, USA) to a final concentration of 50%. ..

    Article Title: A small number of male-biased candidate pheromone receptors are expressed in large subsets of the olfactory sensory neurons in the antennae of drones from the European honey bee Apis mellifera.
    Article Snippet: .. Each slide with tissue sections was covered with 130 μL hybridization solution 1 [50% formamide, 25% H2O, 25% Microarray hybridization solution version 2.0 (GE Healthcare, Freiburg, Germany)] supplemented with the labeled riboprobe. ..

    Expressing:

    Article Title: Expression and Functional Analysis of lncRNAs Involved in Platelet-Derived Growth Factor-BB-Induced Proliferation of Human Aortic Smooth Muscle Cells
    Article Snippet: Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000; 1 μg of each labeled cRNA was fragmented by adding 5 μL of 10 × Blocking Agent and 1 μL of 25 × Fragmentation Buffer and then heated at 60°C for 30 min. .. Finally, 25 μL of 2 × GE Hybridization Buffer was added to dilute the labeled cRNA; 50 μL of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. .. Slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

    Microarray:

    Article Title: Expression and Functional Analysis of lncRNAs Involved in Platelet-Derived Growth Factor-BB-Induced Proliferation of Human Aortic Smooth Muscle Cells
    Article Snippet: Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000; 1 μg of each labeled cRNA was fragmented by adding 5 μL of 10 × Blocking Agent and 1 μL of 25 × Fragmentation Buffer and then heated at 60°C for 30 min. .. Finally, 25 μL of 2 × GE Hybridization Buffer was added to dilute the labeled cRNA; 50 μL of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. .. Slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

    Article Title: Characterization of histopathology and gene-expression profiles of synovitis in early rheumatoid arthritis using targeted biopsy specimens
    Article Snippet: The PCR products were spotted in duplicate on type VII glass slides (Amersham Biosciences) with a Microarray Spotter Generation III (Amersham Biosciences). .. Labeled probes were mixed with Microarray Hybridization Solution Version 2 (Amersham Biosciences) and formamide (Sigma Chemical Co, St Louis, MO, USA) to a final concentration of 50%. ..

    Article Title: A small number of male-biased candidate pheromone receptors are expressed in large subsets of the olfactory sensory neurons in the antennae of drones from the European honey bee Apis mellifera.
    Article Snippet: .. Each slide with tissue sections was covered with 130 μL hybridization solution 1 [50% formamide, 25% H2O, 25% Microarray hybridization solution version 2.0 (GE Healthcare, Freiburg, Germany)] supplemented with the labeled riboprobe. ..

    Article Title: Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer.
    Article Snippet: In brief The mechanisms through which microsatellite-stable colorectal cancer inhibits anti-tumor immunity and resists immune checkpoint blockade are incompletely understood.. Peuker et al. describe a microbiota-dependent pathway of crosstalk between myeloid cells, T cells, and tumor cells that inhibits CD8 T cell-dependent anti-tumor immunity through the co-inhibitory proteins B7H3 and B7H4 and that is amenable to therapeutic targeting.

    Article Title: Snail acetylation by autophagy‐derived acetyl‐coenzyme A promotes invasion and metastasis of KRAS ‐ LKB1 co‐mutated lung cancer cells
    Article Snippet: .. Paraffin sections of human lung adenocarcinoma (LUAD) tissues from a tumor tissue microarray (TMA) containing 92 lung cancer samples and 88 matched normal tissues (HLugA180Su03, US Biomax, Derwood, MD, USA) were were deparaffinized in Bond dewax solution (AR9222, Leica Biosystems, Baden‐Wurttemberg, Germany) and rehydrated in absolute ethanol (1.07017, Merck, Burlington, MA, USA), and antigen retrieval was performed by boiling in 10 mmol/L sodium citrate (pH 6) for 20 min. Epitope retrieval was performed using BOND Epitope Retrieval Solution 2 kits (AR9640, Leica Biosystems). .. Immunofluorescence signals were visualized using an OPAL 7‐Color Automation IHC Kit (NEL82100KT, Akoya Biosciences, Marlborough, MA, USA): tyramide signal amplification (TSA) dyes 520 (1:1200, #HPA029100, rabbit polyclonal anti‐lysosomal associated membrane protein 2 (LAMP2), Atlas Antibodies, Bromma, Stockholms, Sweden, RRID: AB_10795022), 690 (1:400, rabbit polyclonal anti‐acetyl‐lysine), 620 (1:300, #HPA069985, rabbit polyclonal anti‐Snail, Atlas Antibodies, RRID: AB_2732146) and spectral DAPI.

    Article Title: The Sensilla-Specific Expression and Subcellular Localization of SNMP1 and SNMP2 Reveal Novel Insights into Their Roles in the Antenna of the Desert Locust Schistocerca gregaria
    Article Snippet: .. After sectioning, the samples were treated for 20 min at 4 °C with 4% paraformaldehyde dissolved in PBS, washed in PBS for 5 min, and then incubated in 0.2 M HCl for 10 min. After washing the samples two times for 2 min in PBS, the slides were transferred into pre-hybridization solution (5× SSC (0.75 M NaCl, 0.075 M sodium citrate, pH 7.0) and 50% formamide) for 10 min. Next, each slide was covered with 130 μL hybridization solution (50% formamide, 25% H 2 O, 25% Microarray Hybridization Solution Version 2.0 (GE Healthcare, Freiburg, Germany)) containing either the ORCO or the SNMP1 antisense riboprobe. ..

    Concentration Assay:

    Article Title: Characterization of histopathology and gene-expression profiles of synovitis in early rheumatoid arthritis using targeted biopsy specimens
    Article Snippet: The PCR products were spotted in duplicate on type VII glass slides (Amersham Biosciences) with a Microarray Spotter Generation III (Amersham Biosciences). .. Labeled probes were mixed with Microarray Hybridization Solution Version 2 (Amersham Biosciences) and formamide (Sigma Chemical Co, St Louis, MO, USA) to a final concentration of 50%. ..

    Staining:

    Article Title: Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer.
    Article Snippet: In brief The mechanisms through which microsatellite-stable colorectal cancer inhibits anti-tumor immunity and resists immune checkpoint blockade are incompletely understood.. Peuker et al. describe a microbiota-dependent pathway of crosstalk between myeloid cells, T cells, and tumor cells that inhibits CD8 T cell-dependent anti-tumor immunity through the co-inhibitory proteins B7H3 and B7H4 and that is amenable to therapeutic targeting.

    Immunohistochemical staining:

    Article Title: Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer.
    Article Snippet: In brief The mechanisms through which microsatellite-stable colorectal cancer inhibits anti-tumor immunity and resists immune checkpoint blockade are incompletely understood.. Peuker et al. describe a microbiota-dependent pathway of crosstalk between myeloid cells, T cells, and tumor cells that inhibits CD8 T cell-dependent anti-tumor immunity through the co-inhibitory proteins B7H3 and B7H4 and that is amenable to therapeutic targeting.

    Double Staining:

    Article Title: Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer.
    Article Snippet: In brief The mechanisms through which microsatellite-stable colorectal cancer inhibits anti-tumor immunity and resists immune checkpoint blockade are incompletely understood.. Peuker et al. describe a microbiota-dependent pathway of crosstalk between myeloid cells, T cells, and tumor cells that inhibits CD8 T cell-dependent anti-tumor immunity through the co-inhibitory proteins B7H3 and B7H4 and that is amenable to therapeutic targeting.

    Incubation:

    Article Title: The Sensilla-Specific Expression and Subcellular Localization of SNMP1 and SNMP2 Reveal Novel Insights into Their Roles in the Antenna of the Desert Locust Schistocerca gregaria
    Article Snippet: .. After sectioning, the samples were treated for 20 min at 4 °C with 4% paraformaldehyde dissolved in PBS, washed in PBS for 5 min, and then incubated in 0.2 M HCl for 10 min. After washing the samples two times for 2 min in PBS, the slides were transferred into pre-hybridization solution (5× SSC (0.75 M NaCl, 0.075 M sodium citrate, pH 7.0) and 50% formamide) for 10 min. Next, each slide was covered with 130 μL hybridization solution (50% formamide, 25% H 2 O, 25% Microarray Hybridization Solution Version 2.0 (GE Healthcare, Freiburg, Germany)) containing either the ORCO or the SNMP1 antisense riboprobe. ..



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    Transcriptome analyses of the ex vivo cultured P. falciparum parasites . (a) Transcriptomes of the ex-vivo IDC of 6 field isolates (representative set of total 11 transcriptomes generated in this study; Additional file ) from the 3 geographical locations over 48 hour sampling time. The heat maps represent the mean-centered log 2 <t>microarray</t> expression ratios for the P. falciparum genes that were ordered according to the phase calculated by the Fast Fourier Transformation for the reference in vitro IDC transcriptome. (b) Age estimate of the ex vivo culture time points for all 11 field isolates. Each colored box represents age estimate (hpi; shown by numbers outside the circle) of the isolate sample relative to the in vitro reference IDC transcriptome calculated as a best fit Correlation (Spearman rank, see materials and methods). Indicated within each box is the sampling collection time with respect to the first sampling time denoted by 0 h that correspond to the initial sample collection from the infected patients prior to culturing. Sampling times with * represent Spearman Rank correlation value less than 0.35 which indicates a deteriorating synchronicity in the later IDC time points and were excluded from the analysis. Time points included in 3 windows (yellow frame) corresponding to rings at 12-16 hpi, trophozoites at 24 to 28 hpi and schizonts at 32 to 36 hpi were selected for further analysis. (c) Clusters of genes with significant differential expression (p-value < 0.01) between the resistant (grey) and susceptible (orange) parasites at ring (14 hpi), trophozoite (26 hpi) and schizont (34 hpi) stages. Shown are the mean-centered expression log 2 ratios for these genes ranked by the z-score based on the differential expression between the resistant and susceptible isolates. Graphs represent the frequency distribution of the peak abundance time in the IDC transcriptome for each group of genes: over-expressed (red bars), under-expressed (green bars) or no significant change in expression (yellow bars). The grey lines represent the middle of the time IDC interval used for the analysis (e.g. ring, (14 hpi), trophozoite (26 hpi) and schizonts (34 hpi).
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    96
    Thermo Fisher affymetrix microarray solutions
    Transcriptome analyses of the ex vivo cultured P. falciparum parasites . (a) Transcriptomes of the ex-vivo IDC of 6 field isolates (representative set of total 11 transcriptomes generated in this study; Additional file ) from the 3 geographical locations over 48 hour sampling time. The heat maps represent the mean-centered log 2 <t>microarray</t> expression ratios for the P. falciparum genes that were ordered according to the phase calculated by the Fast Fourier Transformation for the reference in vitro IDC transcriptome. (b) Age estimate of the ex vivo culture time points for all 11 field isolates. Each colored box represents age estimate (hpi; shown by numbers outside the circle) of the isolate sample relative to the in vitro reference IDC transcriptome calculated as a best fit Correlation (Spearman rank, see materials and methods). Indicated within each box is the sampling collection time with respect to the first sampling time denoted by 0 h that correspond to the initial sample collection from the infected patients prior to culturing. Sampling times with * represent Spearman Rank correlation value less than 0.35 which indicates a deteriorating synchronicity in the later IDC time points and were excluded from the analysis. Time points included in 3 windows (yellow frame) corresponding to rings at 12-16 hpi, trophozoites at 24 to 28 hpi and schizonts at 32 to 36 hpi were selected for further analysis. (c) Clusters of genes with significant differential expression (p-value < 0.01) between the resistant (grey) and susceptible (orange) parasites at ring (14 hpi), trophozoite (26 hpi) and schizont (34 hpi) stages. Shown are the mean-centered expression log 2 ratios for these genes ranked by the z-score based on the differential expression between the resistant and susceptible isolates. Graphs represent the frequency distribution of the peak abundance time in the IDC transcriptome for each group of genes: over-expressed (red bars), under-expressed (green bars) or no significant change in expression (yellow bars). The grey lines represent the middle of the time IDC interval used for the analysis (e.g. ring, (14 hpi), trophozoite (26 hpi) and schizonts (34 hpi).
    Affymetrix Microarray Solutions, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    NanoView Biosciences microarray chips solution a
    Transcriptome analyses of the ex vivo cultured P. falciparum parasites . (a) Transcriptomes of the ex-vivo IDC of 6 field isolates (representative set of total 11 transcriptomes generated in this study; Additional file ) from the 3 geographical locations over 48 hour sampling time. The heat maps represent the mean-centered log 2 <t>microarray</t> expression ratios for the P. falciparum genes that were ordered according to the phase calculated by the Fast Fourier Transformation for the reference in vitro IDC transcriptome. (b) Age estimate of the ex vivo culture time points for all 11 field isolates. Each colored box represents age estimate (hpi; shown by numbers outside the circle) of the isolate sample relative to the in vitro reference IDC transcriptome calculated as a best fit Correlation (Spearman rank, see materials and methods). Indicated within each box is the sampling collection time with respect to the first sampling time denoted by 0 h that correspond to the initial sample collection from the infected patients prior to culturing. Sampling times with * represent Spearman Rank correlation value less than 0.35 which indicates a deteriorating synchronicity in the later IDC time points and were excluded from the analysis. Time points included in 3 windows (yellow frame) corresponding to rings at 12-16 hpi, trophozoites at 24 to 28 hpi and schizonts at 32 to 36 hpi were selected for further analysis. (c) Clusters of genes with significant differential expression (p-value < 0.01) between the resistant (grey) and susceptible (orange) parasites at ring (14 hpi), trophozoite (26 hpi) and schizont (34 hpi) stages. Shown are the mean-centered expression log 2 ratios for these genes ranked by the z-score based on the differential expression between the resistant and susceptible isolates. Graphs represent the frequency distribution of the peak abundance time in the IDC transcriptome for each group of genes: over-expressed (red bars), under-expressed (green bars) or no significant change in expression (yellow bars). The grey lines represent the middle of the time IDC interval used for the analysis (e.g. ring, (14 hpi), trophozoite (26 hpi) and schizonts (34 hpi).
    Microarray Chips Solution A, supplied by NanoView Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Transcriptome analyses of the ex vivo cultured P. falciparum parasites . (a) Transcriptomes of the ex-vivo IDC of 6 field isolates (representative set of total 11 transcriptomes generated in this study; Additional file ) from the 3 geographical locations over 48 hour sampling time. The heat maps represent the mean-centered log 2 microarray expression ratios for the P. falciparum genes that were ordered according to the phase calculated by the Fast Fourier Transformation for the reference in vitro IDC transcriptome. (b) Age estimate of the ex vivo culture time points for all 11 field isolates. Each colored box represents age estimate (hpi; shown by numbers outside the circle) of the isolate sample relative to the in vitro reference IDC transcriptome calculated as a best fit Correlation (Spearman rank, see materials and methods). Indicated within each box is the sampling collection time with respect to the first sampling time denoted by 0 h that correspond to the initial sample collection from the infected patients prior to culturing. Sampling times with * represent Spearman Rank correlation value less than 0.35 which indicates a deteriorating synchronicity in the later IDC time points and were excluded from the analysis. Time points included in 3 windows (yellow frame) corresponding to rings at 12-16 hpi, trophozoites at 24 to 28 hpi and schizonts at 32 to 36 hpi were selected for further analysis. (c) Clusters of genes with significant differential expression (p-value < 0.01) between the resistant (grey) and susceptible (orange) parasites at ring (14 hpi), trophozoite (26 hpi) and schizont (34 hpi) stages. Shown are the mean-centered expression log 2 ratios for these genes ranked by the z-score based on the differential expression between the resistant and susceptible isolates. Graphs represent the frequency distribution of the peak abundance time in the IDC transcriptome for each group of genes: over-expressed (red bars), under-expressed (green bars) or no significant change in expression (yellow bars). The grey lines represent the middle of the time IDC interval used for the analysis (e.g. ring, (14 hpi), trophozoite (26 hpi) and schizonts (34 hpi).

    Journal: BMC Genomics

    Article Title: Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription

    doi: 10.1186/1471-2164-12-391

    Figure Lengend Snippet: Transcriptome analyses of the ex vivo cultured P. falciparum parasites . (a) Transcriptomes of the ex-vivo IDC of 6 field isolates (representative set of total 11 transcriptomes generated in this study; Additional file ) from the 3 geographical locations over 48 hour sampling time. The heat maps represent the mean-centered log 2 microarray expression ratios for the P. falciparum genes that were ordered according to the phase calculated by the Fast Fourier Transformation for the reference in vitro IDC transcriptome. (b) Age estimate of the ex vivo culture time points for all 11 field isolates. Each colored box represents age estimate (hpi; shown by numbers outside the circle) of the isolate sample relative to the in vitro reference IDC transcriptome calculated as a best fit Correlation (Spearman rank, see materials and methods). Indicated within each box is the sampling collection time with respect to the first sampling time denoted by 0 h that correspond to the initial sample collection from the infected patients prior to culturing. Sampling times with * represent Spearman Rank correlation value less than 0.35 which indicates a deteriorating synchronicity in the later IDC time points and were excluded from the analysis. Time points included in 3 windows (yellow frame) corresponding to rings at 12-16 hpi, trophozoites at 24 to 28 hpi and schizonts at 32 to 36 hpi were selected for further analysis. (c) Clusters of genes with significant differential expression (p-value < 0.01) between the resistant (grey) and susceptible (orange) parasites at ring (14 hpi), trophozoite (26 hpi) and schizont (34 hpi) stages. Shown are the mean-centered expression log 2 ratios for these genes ranked by the z-score based on the differential expression between the resistant and susceptible isolates. Graphs represent the frequency distribution of the peak abundance time in the IDC transcriptome for each group of genes: over-expressed (red bars), under-expressed (green bars) or no significant change in expression (yellow bars). The grey lines represent the middle of the time IDC interval used for the analysis (e.g. ring, (14 hpi), trophozoite (26 hpi) and schizonts (34 hpi).

    Article Snippet: From this, 4 μg of DNA was labeled with fluorescent Cy5 dye and used for the microarray hybridization (GE Amersham, USA).

    Techniques: Ex Vivo, Cell Culture, Generated, Sampling, Microarray, Expressing, Transformation Assay, In Vitro, Infection

    Classification of differentially expressed genes across the whole IDC and validation of differential expression of 5 genes by qPCR . (a) Plot of the Ranked Product Score for all 4,015 genes calculated from the geometric mean of the ranked z-scores of the genes in the 3 stages in the generated transcriptome (orange) and in the randomized dataset (green) (for details see material and methods). The graphs represent 4 over (b) and 4 under-expressed (c) genes in the resistant parasites with potential regulatory functions present in the top 5% of each extreme of the rank product distribution, respectively ((a) grey boxes). Data points represent the mean log 2 expression ratios of the genes in the resistant (green triangle), susceptible Lao and Thai (blue diamond), and susceptible Cambodian isolates (CP022, purple circle) across the three selected stage intervals. The data are projected onto the gene expression profiles analyzed by the in vitro IDC transcriptome (red square). Error bars reflect the standard deviation of the log 2 ratios for each data point. (d) Bars represent the log 2 -transformed fold change measured from relative quantification of a resistant versus a sensitive isolate using PFC0965w as a reference control gene in real-time PCR experiments (teal) and plotted alongside the microarray expression ratios (light blue). Error bars reflect the standard deviation of the log 2 ratios over triplicates.

    Journal: BMC Genomics

    Article Title: Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription

    doi: 10.1186/1471-2164-12-391

    Figure Lengend Snippet: Classification of differentially expressed genes across the whole IDC and validation of differential expression of 5 genes by qPCR . (a) Plot of the Ranked Product Score for all 4,015 genes calculated from the geometric mean of the ranked z-scores of the genes in the 3 stages in the generated transcriptome (orange) and in the randomized dataset (green) (for details see material and methods). The graphs represent 4 over (b) and 4 under-expressed (c) genes in the resistant parasites with potential regulatory functions present in the top 5% of each extreme of the rank product distribution, respectively ((a) grey boxes). Data points represent the mean log 2 expression ratios of the genes in the resistant (green triangle), susceptible Lao and Thai (blue diamond), and susceptible Cambodian isolates (CP022, purple circle) across the three selected stage intervals. The data are projected onto the gene expression profiles analyzed by the in vitro IDC transcriptome (red square). Error bars reflect the standard deviation of the log 2 ratios for each data point. (d) Bars represent the log 2 -transformed fold change measured from relative quantification of a resistant versus a sensitive isolate using PFC0965w as a reference control gene in real-time PCR experiments (teal) and plotted alongside the microarray expression ratios (light blue). Error bars reflect the standard deviation of the log 2 ratios over triplicates.

    Article Snippet: From this, 4 μg of DNA was labeled with fluorescent Cy5 dye and used for the microarray hybridization (GE Amersham, USA).

    Techniques: Expressing, Generated, In Vitro, Standard Deviation, Transformation Assay, Real-time Polymerase Chain Reaction, Microarray

    CGH analysis of artemisinin resistant isolates, Genotyping of isolates and Sequencing of drug-resistant genes to determine haplotypes . (a) The heat map represents hierarchical clustering of CGH signal (against 3d7 genome) for 257 microarray oligonucleotide elements representing 138 genes in 93 CNV regions identified by GADA analysis (see material and methods). (b) Visualization of msp1 , msp2 and glurp nested PCR products of the 6 isolates on a 2.5% agarose gel shows distinctive patterns of product sizes for each clone, except for CP025 and CP037. (c) Tables depict the commonly and rarely found single nucleotide polymorphisms (SNPs) found based on the codon position (top row) and the sequenced bases of the various isolates and corresponding amino acid in brackets. Highlighted in yellow are the codons with mutations compared to wild type 3d7.

    Journal: BMC Genomics

    Article Title: Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription

    doi: 10.1186/1471-2164-12-391

    Figure Lengend Snippet: CGH analysis of artemisinin resistant isolates, Genotyping of isolates and Sequencing of drug-resistant genes to determine haplotypes . (a) The heat map represents hierarchical clustering of CGH signal (against 3d7 genome) for 257 microarray oligonucleotide elements representing 138 genes in 93 CNV regions identified by GADA analysis (see material and methods). (b) Visualization of msp1 , msp2 and glurp nested PCR products of the 6 isolates on a 2.5% agarose gel shows distinctive patterns of product sizes for each clone, except for CP025 and CP037. (c) Tables depict the commonly and rarely found single nucleotide polymorphisms (SNPs) found based on the codon position (top row) and the sequenced bases of the various isolates and corresponding amino acid in brackets. Highlighted in yellow are the codons with mutations compared to wild type 3d7.

    Article Snippet: From this, 4 μg of DNA was labeled with fluorescent Cy5 dye and used for the microarray hybridization (GE Amersham, USA).

    Techniques: Sequencing, Microarray, Nested PCR, Agarose Gel Electrophoresis