Journal: Journal of Thoracic Disease

Article Title: Diagnostic performance of DNA microarray for detecting rifampicin and isoniazid resistance in Mycobacterium tuberculosis

doi: 10.21037/jtd-21-913

Figure Lengend Snippet: The ROC curve of the CapitalBio DNA microarray for detecting RFP resistance. ROC, receiver operating characteristic; RFP, rifampicin.

Article Snippet: The kappa coefficient between the DNA microarray and the liquid culture was 0.75 (95% CI: 0.70–0.80; ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 The ROC curve of the CapitalBio DNA microarray for detecting INH resistance.

Techniques: Microarray

Journal: Journal of Thoracic Disease

Article Title: Diagnostic performance of DNA microarray for detecting rifampicin and isoniazid resistance in Mycobacterium tuberculosis

doi: 10.21037/jtd-21-913

Figure Lengend Snippet: Diagnostic performance of DNA microarray for RFP resistance

Article Snippet: The kappa coefficient between the DNA microarray and the liquid culture was 0.75 (95% CI: 0.70–0.80; ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 The ROC curve of the CapitalBio DNA microarray for detecting INH resistance.

Techniques: Diagnostic Assay, Microarray

Journal: Journal of Thoracic Disease

Article Title: Diagnostic performance of DNA microarray for detecting rifampicin and isoniazid resistance in Mycobacterium tuberculosis

doi: 10.21037/jtd-21-913

Figure Lengend Snippet: The ROC curve of the CapitalBio DNA microarray for detecting INH resistance. ROC, receiver operating characteristic; IHN, isonicotinic acid hydrazide.

Article Snippet: The kappa coefficient between the DNA microarray and the liquid culture was 0.75 (95% CI: 0.70–0.80; ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 The ROC curve of the CapitalBio DNA microarray for detecting INH resistance.

Techniques: Microarray

Journal: Journal of Thoracic Disease

Article Title: Diagnostic performance of DNA microarray for detecting rifampicin and isoniazid resistance in Mycobacterium tuberculosis

doi: 10.21037/jtd-21-913

Figure Lengend Snippet: Diagnostic performance of DNA microarray for INH resistance

Article Snippet: The kappa coefficient between the DNA microarray and the liquid culture was 0.75 (95% CI: 0.70–0.80; ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 The ROC curve of the CapitalBio DNA microarray for detecting INH resistance.

Techniques: Diagnostic Assay, Microarray

Journal: Journal of the American Chemical Society

Article Title: Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology

doi: 10.1021/jacs.6b10646

Figure Lengend Snippet: Schematic of SomaLogic proteomics assay.97 Step 1: Biotin (B), photolinker (L), and fluorophore (F)-labeled SOMAmers (A) bind with cognate target proteins (T). Step 2: SOMAmer–protein complexes are captured by streptavidin (SA)-coated magnetic beads, followed by washing unbound proteins and addition of secondary biotin on captured proteins. Step 3: UV irradiation cleaves the photolinker, and non-specifically bound protein is removed using competitive buffer. Step 4: Biotin-labeled proteins are captured by secondary SA-coated magnetic beads. Step 5: Aptamers are eluted. Step 6: DNA microarray analysis is used to quantitate the protein.

Article Snippet: The eluted aptamers are then subjected to DNA microarray to determine the identities and corresponding proteins. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Schematic of SomaLogic proteomics assay.

Techniques: Labeling, Magnetic Beads, Irradiation, Microarray

Journal: Seminars in respiratory and critical care medicine

Article Title: Evolving Concepts in Lung Carcinogenesis

doi: 10.1055/s-0031-1272867

Figure Lengend Snippet: Examples of High-Throughput Techniques for Molecular Analyses

Article Snippet: These changes encompass DNA methylation, histone modifications/chromatin changes, and miRNA level alterations, and they play a vital role in the regulation of gene expression ( ). table ft1 table-wrap mode="anchored" t5 caption a7 Analyte High-Throughput Methods Genomics Whole genome sequencing, CGH arrays, SNP arrays Epigenomics miRNA microarrays/sequencing, DNA methylation arrays/sequencing (MeDIP, or bisulfite conversion) Transcriptomics RNA-sequencing, gene expression microarrays Proteomics Two-dimensional gel electrophoresis, MALDI-TOF MS, tandem MS, protein arrays, tissue microarrays Open in a separate window CGH, comparative genomic hybridization; SNP, single-nucleotide polymorphism; miRNA, microRNA; MeDIP, methylation dependent immunoprecipitation; MALDI-TOF MS, matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Techniques: Sequencing, DNA Methylation Assay, Methylated DNA Immunoprecipitation, Gene Expression, Two-Dimensional Gel Electrophoresis

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: A novel pharmacologic activity of ketorolac for therapeutic benefit in ovarian cancer patients

doi: 10.1158/1078-0432.CCR-15-0461

Figure Lengend Snippet: Tissuescan ovarian cancer cDNA microarrays (Origene) were amplified using primers against Rac1, Rac1b, Cdc42, RhoA, and β-actin as described in methods. As per the manufacturer's description, patients with endometriosis, leiomyoma of myometrium, follicular cysts, abscesses, or secretory endometrium, but otherwise healthy ovarian tissue, were considered normal (n=19). Tissues defined as low grade have a FIGO score of 1 (n=19) or 2 (n=32). Tissues considered high grade have a FIGO score of 3 (n=60) or 4 (n=9). The cDNAs of 10 patients were excluded due to a lack of grade information. Clinical characteristics of the samples in the array are provided in Supplemental Table S2. Groups were compared to normal using a two-tailed t-test, and significant increase in Rac1b was detected. * indicates significance is p≤0.05. Serous only, analysis by grade is reported in Supplemental Figure S1.

Article Snippet: For Cdc42 one way non-parametric ANOVA (p=0.0001) and Tukey's post-test shows normal stroma and benign to borderline tumor vs. intermediate to high grade carcinoma p<0.05 with all other comparisons non-significant. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 caption a8 Expression of constitutively active Rac1b mRNA is elevated in ovarian cancer specimens Tissuescan ovarian cancer cDNA microarrays (Origene) were amplified using primers against Rac1, Rac1b, Cdc42, RhoA, and β-actin as described in methods.

Techniques: Amplification, Two Tailed Test

Journal:

Article Title: Protein Binding Microarrays for the Characterization of Protein-DNA Interactions

doi:

Figure Lengend Snippet: Identical portions of yeast intergenic microarrays printed onto Corning® GAPS II slides, processed in different ways (see below) before UV-crosslinking, and then stained with SYBR Green I. Images have been false-colored as in Figure 2. Examples of microarrays with poor spot quality are shown in (a) and (b). In both of these cases, the DNA is distributed non-uniformly, with either (a) high concentrations near the centers of spots, or (b) high concentrations along spot perimeters. Both of these microarrays resulted from two separate print runs, from which microarrays were UV-crosslinked without first rehydrating and baking. An example of a good quality microarray is shown in (c). This microarray was rehydrated and then baked before being UV-crosslinked. (Reproduced from [42] with permission from The Humana Press, Inc.)

Article Snippet: Various additional filtering criteria can be applied later during data analysis to remove from consideration any remaining spots that may be noisy even after removing spots with highly variable pixel signal intensities. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 4 caption a7 caption a8 Examples of DNA microarray spot quality Identical portions of yeast intergenic microarrays printed onto Corning® GAPS II slides, processed in different ways (see below) before UV-crosslinking, and then stained with SYBR Green I.

Techniques: Staining, SYBR Green Assay, Microarray

Journal:

Article Title: Butyrate Greatly Enhances Derivation of Human Induced Pluripotent Stem Cells by Promoting Epigenetic Remodeling and the Expression of Pluripotency-Associated Genes

doi: 10.1002/stem.402

Figure Lengend Snippet: Butyrate enhanced promoter DNA demethylation of pluripotency-associated genes. (A): We used Infinium HumanMethylation27 Bead-Chip to analyze the DNA methylome before and after successfully reprogramming. The level of DNA methylation (from 0 to 1) at gene promoters containing a CpG island (white) or without (black) is illustrated by color from blue to red. Loci are grouped as four clusters based on loss (#2), gain (#3), or unchanged (#1 remaining high and #4 remaining low) of DNA methylation. We used the K-means clustering algorithm to analyze the methylation data from three fibroblast lines (IMR90, MSC1640, and BASC), eight successfully reprogrammed iPS cells, and two ES lines (H1 and H9). The eight validated iPS cells showed a pattern highly similar to hES cells versus their parental fibroblasts. (B): Multidimensional scaling analysis of the relationship among different cell types based on DNA methylation profiles of 1,174 loci in cluster #2 was performed. Data along the first two components are plotted here. Two types of mesenchymal stem cells (MSCs) (MSC1640 and BASC), derived iPS cell lines, and intermediate cells during MSC reprogramming at day 6 (D6, condition #1) or day 12 (D12, condition #2) with or without sodium butyrate (N) were used. Duplicate intermediate MSC samples are referred by s1 and s2. It is evident that the butyrate-treated samples at day 12 (D12N2, red arrow) cluster away from MSCs and move closer to the iPS/ES group. (C): Detection of CpG DNA methylation by the microarray (numbers for 0 to 1.00) and by direct sequencing after bisulfite conversion (filled circles) of the promoter regions of POU5F1/OCT4 and DPPA2 genes. Reduction of DNA methylation in multiple CpG sites at both promoters is evident from parental MSCs to reprogramming intermediate cells at 12 (especially after butyrate treatment) and ultimately in successfully reprogrammed iPS cells. (D): DPPA2 transgene expression partially substitutes butyrate and further enhances reprogramming by the four reprogramming factors OSKM. BASC or IMR90 cells were transduced by a retroviral vector expressing either DPPA2 or GFP (as a control) together with OSKM, and fold change in TRA-1-60+ colonies was enumerated (mean ± SEM, n = 4). Abbreviations: BASC, Bone marrow Aspirate derived marrow Stromal Cells from patient with Sickle Cell Disease; GFP, green fluorescent protein; ES, ES, embryonic stem; hES, human embryonic stem; iPS, induced pluripotent stem; n, number; N, sodium butyrate; OSKM, Oct4, Sox2, Klf4, and c-Myc collectively.

Article Snippet: These results are consistent with an earlier report about the murine system comparing ES and differentiated cells [ 16 ] and a recent report comparing DNA methylation in human somatic cells, iPS cells, and ES cells using a different platform [ 17 ]. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Butyrate enhanced promoter DNA demethylation of pluripotency-associated genes. (A): We used Infinium HumanMethylation27 Bead-Chip to analyze the DNA methylome before and after successfully reprogramming.

Techniques: DNA Methylation Assay, Methylation, Derivative Assay, Microarray, Sequencing, Expressing, Plasmid Preparation

Journal:

Article Title: Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays

doi: 10.1093/nar/gkg806

Figure Lengend Snippet: Gene expression analysis of the L.tarentolae As50.1 mutant as determined by DNA microarrays and northern blot analysis. (A) Scatter plot of hybridisation intensities between TarAs50.1 (Cy5) and wild-type L.tarentolae cells (Cy3). The expression of genes represented by dots within the dashed lines are considered as similar in the two tested strains. Dashed lines indicate 2-fold differences and genes whose expression differ significantly are indicated. (B) Confirmation of DNA microarray results by northern blot analysis showing that PGPA and GSH1 were overexpressed in the same mutant. Presumably, for genes grossly overexpressed, microarray results can only be qualitative as the signals are rapidly saturated. An α-tubulin hybridisation was performed to monitor RNA and DNA loading. For each figure we show one representative of several control gels used for the various genes. For quantification see Table ​Table2.2. (C) Southern blot analysis to test whether increased RNA expression is mediated, at least in part, by gene amplification. The DNA of the parasites was digested with HindIII. 1, L.tarentolae wild-type cell; 2, TarII As50.1. Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen.

Article Snippet: Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Average fold increase compared to wild-type cells Strains Genes Microarrays Northern Southern TarAs50.1 GSH1 3.0 ± 0.2* a 10.9 12.9 PGPA 2.0 ± 0.3** b 15 3.2 TarIISbIII400.1 GSH1 11.5 ± 0.9* 44.7 3.9 (1.9 ± 0.1*) c PGPA 2.2 ± 0.3** 2.9 12.7 (6.2 ± 0.5*) c GSH2 2.8 ± 0.3* 3.6 0.8 (1.0) c SAHH 0.7 ± 0.1** 1.1 2.2(2.8 ± 0.1*) c LV39 MTX60.2 PTR1 25.3 ± 4.0* 20 17.2 MAT2 4.1 ± 0.2* 4 1.1 LV39 MTX60.4 FT 0.6* 0.12 d 0 e DHFR 2.8 ± 0.1* 11.5 7.1 Open in a separate window a * P value <0.0001. b ** P value <0.02. c Values within parenthesis correspond to gene amplification as determined using DNA microarrays. d This signal is probably coming from one of the several other FT members. e Some of the copy number of the FT family remains unchanged but other genes, indicated by asterisks, were deleted. caption a8 Correlation between microarray results, RNA expression and DNA copy number The antimonite resistant mutant L.tarentolae TarIISbIII400.1 has been described previously.

Techniques: Expressing, Mutagenesis, Northern Blot, Hybridization, Microarray, Southern Blot, RNA Expression, Amplification

Journal:

Article Title: Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays

doi: 10.1093/nar/gkg806

Figure Lengend Snippet: Gene expression analysis of the L.tarentolae TarIISbIII400.1 mutant as determined by DNA microarrays and northern blot analysis. (A) Scatter plot of hybridisation intensities between Tar SbIII400.1 (Cy5) and wild-type L.tarentolae cells (Cy3). Dashed lines indicate 2-fold differences. (B) Confirmation of DNA microarray results by northern blot analysis showing that PGPA, GSH1 and GSH2 are overexpressed. An α-tubulin hybridisation was performed to monitor RNA and DNA loading. For each figure we show one representative of several control gels used for the various genes. For quantification see Table ​Table2.2. (C) Southern blot analysis to test whether increased RNA expression is mediated by gene amplification. The DNA of the parasites was digested with HindIII (blots hybridised to GSH2 and tubulin probes); EcoRI (blot hybridised to a GSH1 probe); and BamHI (blot hybridised to a PGPA probe). 1, Leishmania tarentolae wild-type cell; 2, TarIISbIII400.1. Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen.

Article Snippet: Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Average fold increase compared to wild-type cells Strains Genes Microarrays Northern Southern TarAs50.1 GSH1 3.0 ± 0.2* a 10.9 12.9 PGPA 2.0 ± 0.3** b 15 3.2 TarIISbIII400.1 GSH1 11.5 ± 0.9* 44.7 3.9 (1.9 ± 0.1*) c PGPA 2.2 ± 0.3** 2.9 12.7 (6.2 ± 0.5*) c GSH2 2.8 ± 0.3* 3.6 0.8 (1.0) c SAHH 0.7 ± 0.1** 1.1 2.2(2.8 ± 0.1*) c LV39 MTX60.2 PTR1 25.3 ± 4.0* 20 17.2 MAT2 4.1 ± 0.2* 4 1.1 LV39 MTX60.4 FT 0.6* 0.12 d 0 e DHFR 2.8 ± 0.1* 11.5 7.1 Open in a separate window a * P value <0.0001. b ** P value <0.02. c Values within parenthesis correspond to gene amplification as determined using DNA microarrays. d This signal is probably coming from one of the several other FT members. e Some of the copy number of the FT family remains unchanged but other genes, indicated by asterisks, were deleted. caption a8 Correlation between microarray results, RNA expression and DNA copy number The antimonite resistant mutant L.tarentolae TarIISbIII400.1 has been described previously.

Techniques: Expressing, Mutagenesis, Northern Blot, Hybridization, Microarray, Southern Blot, RNA Expression, Amplification

Journal:

Article Title: Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays

doi: 10.1093/nar/gkg806

Figure Lengend Snippet: Gene expression analysis of the L.major LV39 MTX60.2 mutant as determined by DNA microarrays and northern blot analysis. (A) Scatter plot of hybridisation intensities between LV39 MTX60.2 (Cy5) and wild-type L.major LV39 cells (Cy3). Dashed lines indicate 2-fold differences. A number of fragments spanning ABC transporter genes cross-hybridised to the overexpressed PGPA. (B) Confirmation of DNA microarray results by northern blot analysis showing overexpression of PTR1 and MAT2. An α-tubulin hybridisation was performed to monitor RNA and DNA loading. For quantification see Table ​Table2.2. (C) Southern blot analysis to test whether increased RNA expression is mediated by gene amplification. The DNA of the parasites was digested with HindIII except for the blot hybridised to the PTR1 probe where the DNA was digested with SacI. 1, Leishmania major wild-type cell; 2, L.major LV39 MTX60.2. Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen.

Article Snippet: Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Average fold increase compared to wild-type cells Strains Genes Microarrays Northern Southern TarAs50.1 GSH1 3.0 ± 0.2* a 10.9 12.9 PGPA 2.0 ± 0.3** b 15 3.2 TarIISbIII400.1 GSH1 11.5 ± 0.9* 44.7 3.9 (1.9 ± 0.1*) c PGPA 2.2 ± 0.3** 2.9 12.7 (6.2 ± 0.5*) c GSH2 2.8 ± 0.3* 3.6 0.8 (1.0) c SAHH 0.7 ± 0.1** 1.1 2.2(2.8 ± 0.1*) c LV39 MTX60.2 PTR1 25.3 ± 4.0* 20 17.2 MAT2 4.1 ± 0.2* 4 1.1 LV39 MTX60.4 FT 0.6* 0.12 d 0 e DHFR 2.8 ± 0.1* 11.5 7.1 Open in a separate window a * P value <0.0001. b ** P value <0.02. c Values within parenthesis correspond to gene amplification as determined using DNA microarrays. d This signal is probably coming from one of the several other FT members. e Some of the copy number of the FT family remains unchanged but other genes, indicated by asterisks, were deleted. caption a8 Correlation between microarray results, RNA expression and DNA copy number The antimonite resistant mutant L.tarentolae TarIISbIII400.1 has been described previously.

Techniques: Expressing, Mutagenesis, Northern Blot, Hybridization, Microarray, Over Expression, Southern Blot, RNA Expression, Amplification

Journal:

Article Title: Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays

doi: 10.1093/nar/gkg806

Figure Lengend Snippet: Gene expression analysis of the L.major LV39 MTX60.4 mutant as determined by DNA microarrays and northern blot analysis. (A) Scatter plot of hybridisation intensities between LV39 MTX 60.4 (Cy3) and wild-type L.major LV39 cells (Cy5). Dashed lines indicate 2-fold limits. (B) Confirmation of DNA microarray results by northern blot analysis showing overexpression of DHFR-TS, while the expression of one member of the FT family labelled with an asterisk is repressed. An α-tubulin hybridisation was performed for the determination of equal RNA and DNA loading. For quantification see Table ​Table2.2. (C) Southern blot analysis to test whether variation in RNA expression is mediated by variation in gene’s copy number. The DNA of the parasites was digested with SalI for the FT and α-tubulin blots and with SacI for the DHFR-TS blot. 1, Leishmania major wild-type cell; 2, L.major LV39 MTX60.4. Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen. (D) Transport experiment showing a decrease in MTX accumulation in the mutant LV39 MTX60.4 cells (filled squares) compared with wild-type L.major LV39 cells (open circles).

Article Snippet: Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Average fold increase compared to wild-type cells Strains Genes Microarrays Northern Southern TarAs50.1 GSH1 3.0 ± 0.2* a 10.9 12.9 PGPA 2.0 ± 0.3** b 15 3.2 TarIISbIII400.1 GSH1 11.5 ± 0.9* 44.7 3.9 (1.9 ± 0.1*) c PGPA 2.2 ± 0.3** 2.9 12.7 (6.2 ± 0.5*) c GSH2 2.8 ± 0.3* 3.6 0.8 (1.0) c SAHH 0.7 ± 0.1** 1.1 2.2(2.8 ± 0.1*) c LV39 MTX60.2 PTR1 25.3 ± 4.0* 20 17.2 MAT2 4.1 ± 0.2* 4 1.1 LV39 MTX60.4 FT 0.6* 0.12 d 0 e DHFR 2.8 ± 0.1* 11.5 7.1 Open in a separate window a * P value <0.0001. b ** P value <0.02. c Values within parenthesis correspond to gene amplification as determined using DNA microarrays. d This signal is probably coming from one of the several other FT members. e Some of the copy number of the FT family remains unchanged but other genes, indicated by asterisks, were deleted. caption a8 Correlation between microarray results, RNA expression and DNA copy number The antimonite resistant mutant L.tarentolae TarIISbIII400.1 has been described previously.

Techniques: Expressing, Mutagenesis, Northern Blot, Hybridization, Microarray, Over Expression, Southern Blot, RNA Expression

Journal:

Article Title: Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays

doi: 10.1093/nar/gkg806

Figure Lengend Snippet: Gene amplification events in L.tarentolae TarIISbIII400.1 as determined by DNA microarrays. (A) Scatter plot of hybridisation intensities between TarIISbIII400.1 and wild-type digested total DNA and labelled, respectively, with Cy5 and Cy3. This corresponds to a second generation of array with 50 genes each spotted 12 times. Dots outside the dotted lines representing 2-fold differences suggest changes in copy number in the mutant. (B) Northern blot analysis of the SAHH gene. 1, Leishmania tarentolae wild-type cell; 2, TarIISbIII400.1. Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen. (C) The amplification of the SAHH gene in this mutant was confirmed by Southern blot of DNA digested with HindIII, while the other amplification events are shown in Figure ​Figure33.

Article Snippet: Sizes were determined using the 1 kb Plus DNA ladder and the 0.24–9.5 kb RNA ladder from Invitrogen. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Average fold increase compared to wild-type cells Strains Genes Microarrays Northern Southern TarAs50.1 GSH1 3.0 ± 0.2* a 10.9 12.9 PGPA 2.0 ± 0.3** b 15 3.2 TarIISbIII400.1 GSH1 11.5 ± 0.9* 44.7 3.9 (1.9 ± 0.1*) c PGPA 2.2 ± 0.3** 2.9 12.7 (6.2 ± 0.5*) c GSH2 2.8 ± 0.3* 3.6 0.8 (1.0) c SAHH 0.7 ± 0.1** 1.1 2.2(2.8 ± 0.1*) c LV39 MTX60.2 PTR1 25.3 ± 4.0* 20 17.2 MAT2 4.1 ± 0.2* 4 1.1 LV39 MTX60.4 FT 0.6* 0.12 d 0 e DHFR 2.8 ± 0.1* 11.5 7.1 Open in a separate window a * P value <0.0001. b ** P value <0.02. c Values within parenthesis correspond to gene amplification as determined using DNA microarrays. d This signal is probably coming from one of the several other FT members. e Some of the copy number of the FT family remains unchanged but other genes, indicated by asterisks, were deleted. caption a8 Correlation between microarray results, RNA expression and DNA copy number The antimonite resistant mutant L.tarentolae TarIISbIII400.1 has been described previously.

Techniques: Amplification, Hybridization, Mutagenesis, Northern Blot, Southern Blot

Journal:

Article Title: Gene Expression in Asthmatic Airway Smooth Muscle

doi: 10.1513/pats.200705-059VS

Figure Lengend Snippet: GENE EXPRESSION STUDIES USING CULTURED AIRWAY SMOOTH MUSCLE CELLS

Article Snippet: More recently, microarrays have been applied to study asthma therapy by investigating the effects of β-agonists on gene expression in cultured airway smooth muscle cells ( 29 ). table ft1 table-wrap mode="anchored" t5 TABLE 2. caption a7 Author ( Reference No. ) Source of Cells Exposures Method of Gene Expression Profiling Findings Lee and coworkers ( 28 ) Commercially available human airway smooth muscle cells IL-13 (100 ng/ml) Affymetrix Genechip HuGeneFL arrays coding for ∼6,500 human genes 204 Genes induced two-fold, including smooth muscle MHC, phospholipase A2, diacyglycerol kinase δ, and IL-13Rα1 Syed and coworkers ( 30 ) 3 Lung transplant donors IL-13 (10–100 ng/ml) Research Genetics and Incyte Genomics cDNA microarrays coding for 8,159 genes A large number of genes induced 1.5-fold or by FDR analyses (total no. not given), including VCAM1, IL-13Rα2, Tenascin C, and histamine receptor H1 IL-13R130Q * Jarai and coworkers ( 27 ) 2 Patients undergoing lung resection IL-13 † Affymetrix HG-U95Av2 microarrays coding for ∼12,500 genes H1 receptor and tenascin were highly induced by IL-13 TGF-β † IL-1β † McGraw and coworkers ( 29 ) Wild-type and transgenic mice overexpressing β 2 -adrenergic receptor None University of Cincinnati Genomic and Microarray Laboratory array coding for 8,734 cDNAs 319 Genes induced 164 Repressed (including phospholamban) Open in a separate window Definition of abbreviations: FDR = false discovery rate; IL-13Rα1 = IL-13 receptor α1; MHC = myosin heavy chain; RT-PCR = reverse transcription–polymerase chain reaction; TGF = transforming growth factor; VCAM = vascular cell adhesion molecule.

Techniques: Expressing, Cell Culture, Transgenic Assay, Microarray