Transcriptional Response of Mycobacterium tuberculosis H37Rv to Bedaquiline
ABSTRACT: Bacteria commonly adapt to stresses by altering gene expression. To understand the response of M. tuberculosis (MTB) to bedaquiline, we performed transcriptomics over a time-course on MTB bacilli exposed to the drug. Overall design: Bacteria were harvested at 1, 6, 24, 48, 96 hrs after being exposed to concentrations of bedaquiline (no drug, 1.5μM, 15μM) during a 7-day drug exposure time course experiment (as indicated in each sample title). RNA was isolated and applied to custom Agilent tiled arrays. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel (Cy3 and Cy5 signals are calculated). Therefore, there are two sample records per each raw data file and the raw data file associated with each sample is indicated in the corresponding sample description field.
Project description:Transcriptional profiling of SMMC-7721 cells comparing control untreated with sub-lethal heat treated cells (50°C for 10 min). Differentially expressed lncRNA and mRNA were measured with an Agilent Human lncRNA+mRNA Array V4.0 (4 × 180 K format) containing 41,000 lncRNAs and 34,000 mRNAs. Goal was to determine the effects of sub-lethal heat treatment on global hepatoma carcinoma cells gene expression. Overall design: Two-condition experiment, sub-lethal heat treated vs. untreated cells. Biological replicates: 3 control replicates, 3 experimental replicates. Please note that experiments were carried out technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the data was processed as though they are single channel (Cy3 and Cy5 signals are calculated insted of Cy3/Cy5 ratios). Therefore three raw data files (for total 6 samples) are linked as Series supplementary files and the corresponding raw data file is indicated in the sample description field.
Project description:Many long noncoding transcripts are involved in cancer progression. Here, we utilized high-throughput microarray to compare the transcriptome alterations between the SNHG1 knockdown or control in HCT116 cell lines. Two independent siRNAs were designed against the SNHG1 cDNA sequence. Thus, we identified 302 genes which were expressionally changed. Moreover, Gene Ontology and pathway enrichment analysis revealed that several gene signature were significantly enriched, such as MAPK signaling pathway, growth factor activity and transcriptional corepresssor activity. Further, GSEA analysis suggested NF-kB signaling pathway, PI3K/Akt pathway were markedly associated with SNHG1-reuglated genes. The present study indicated that SNGH1 regulated both the local and distal genes in cancer progression. Overall design: HCT116 cells with SNHG1 knockdown and control. Three biological replicates of each condition were analyzed on Agilent microarray. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated). Thus, the raw data files (one file per two sample records) were linked as Series supplementary file and are indicated in the corresponding sample 'description' field.
Project description:Covalent heterodimers of the Cy3 and Cy5 fluorophores have been prepared from commercially available starting materials and characterized at the single-molecule level. This system behaves as a discrete molecular photoswitch, in which photoexcitation of the Cy5 results in fluorescence emission or, with a much lower probability, causes the Cy5 to enter into a long-lived, but metastable, dark state. Photoinduced recovery of the emissive Cy5 is achieved by very low intensity excitation (5 W cm(-2)) of the Cy3 fluorophore at a shorter wavelength. A similar system consisting of proximal, but not covalently linked, Cy3 and Cy5 has found application in stochastic optical reconstruction microscopy (STORM), a single-molecule localization-based technique for super-resolution imaging that requires photoswitching. The covalent Cy3-Cy5 heterodimers described herein eliminate the need for probabilistic methods of situating the Cy3 and Cy5 in close proximity to enable photoswitching. As proof of principle, these heterodimers have been applied to super-resolution imaging of the tubular stalk structures of live Caulobacter crescentus bacterial cells.
Project description:We screened for the changes in gene expression induced by an LSD1 inhibitor to elucidate the mechanism of its cytotoxic effect on T-cell acute lymphoblastic leukemia (T-ALL). Overall design: We isolated mRNA from the T-ALL cell line MOLT4 cultured with vehicle alone or LSD1 inhibitor, and subjected them to gene expression profiling using an Agilent GeneChip Array. Please note that experiments were technically performed as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed dat was provided for each single channel (Cy3 and Cy5 signals; i.e. one raw data file for two sample records).
Project description:To understand the response of M. tuberculosis (MTB) to the drug BTZ043, we performed transcriptomics on MTB bacilli exposed to the drug. Overall design: Bacteria were harvested at 0,1 day after being exposed to concentrations of BTZ043 (no drug, 0.006μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.
Project description:Long noncoding RNAs (lncRNAs), which are noncoding RNAs (ncRNAs) with length more than 200 nucleotides (nt), have been demonstrated to be involved in various types of cancer. In this study, a custom designed microarray platform covering both mRNAs and lncRNAs was applied to tumor tissues of gastric, colon, liver and lung. 316 and 157 differential expressed (DE-) protein coding genes and lncRNAs common to these four types of cancer were identified respectively. Overall design: The expression profiles of cancer and adjacent normal tissues form 76 patients (20 with gastric cancer, 20 with colon cancer, 16 with liver cancer and 20 with lung cancer) were studied by microarray and a set of lncRNAs as well as PCGs were identified as potential biomarkers general to different types of cancer. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed though they are single channel (total 152 sample records for 76 raw data files; Cy3 and Cy5 signals are calculated). Therefore, raw data file for each sample was duplicated and linked to each paired sample records. For example, the raw data files for the 'Normal_tissue_Colon_cancer_patient_01'(Cy5) sample and 'Cancer_tissue_Colon_cancer_patient_01'(Cy3) sample are identical.
Project description:To understand the response of M. tuberculosis (MTB) to the first-line drug P218, we performed transcriptomics on MTB bacilli exposed to the drug. Overall design: Bacteria were harvested at 0,1 day after being exposed to concentrations of P218 (no drug, 0.1μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.
Project description:To understand the response of M. tuberculosis (MTB) to the first-line drug clarithromycin, we performed transcriptomics on MTB bacilli exposed to the drug. Overall design: Bacteria were harvested at 0,1 day after being exposed to concentrations of clarithromycin (no drug, 20μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.
Project description:We have synthesized fluorescent DNA duplexes featuring multiple thiazole orange (TO) intercalating dyes covalently attached to the DNA via a triazole linkage. The intercalating dyes stabilize the duplex against thermal denaturation and show bright fluorescence in the green region of the spectrum. The emission color can be changed to orange or red by addition of energy-accepting Cy3 or Cy5 dyes attached covalently to the DNA duplex. The dye-modified DNA duplexes were then attached to a secondary antibody for intracellular fluorescence imaging of centrosomes in Drosophila embryos. Bright fluorescent foci were observed at the centrosomes in both the donor (TO) and acceptor (Cy5) channels, because the energy transfer efficiency is moderate. Monitoring the Cy5 emission channel significantly minimized the background signal because of the large shift in emission wavelength allowed by energy transfer.
Project description:To develop structural modifications of dNTPs that are compatible with Taq DNA polymerase activity, we synthesized eight dUTP derivatives conjugated with Cy3 or Cy5 dye analogues that differed in charge and charge distribution throughout the fluorophore. These dUTP derivatives and commercial Cy3- and Cy5-dUTP were studied in Taq polymerase-dependent polymerase chain reactions (PCRs) and in primer extension reactions using model templates containing one, two and three adjacent adenine nucleotides. The relative amounts of amplified DNA and the kinetic parameters Km and Vmax characterizing the incorporation of labelled dUMPs have been estimated using fluorescence measurements and analysed. The dUTPs labelled with electroneutral zwitterionic analogues of Cy3 or Cy5 fluorophores were used by Taq polymerase approximately one order of magnitude more effectively than the dUTPs labelled with negatively charged analogues of Cy3 or Cy5. The nucleotidyl transferase activity of Taq polymerase was also observed and resulted in the addition of dUMPs labelled with electroneutral or positively charged fluorophores to the 3' ends of DNA. The introduction of mutually compensating charges into fluorophores or other functional groups conjugated to dNTPs can be considered a basis for the creation of PCR-compatible modified nucleoside triphosphates.