Project description:To determine Sigma 54 (SigL) reglons in Bacillus thuringiensis HD73 strain, A sigLmutant, HD(ΔsigL::kan), was constructed with insertion of kanamycin resistance gene cassete. We have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between mutant and wild-type strains.
Project description:To determine Sigma 54 (SigL) reglons in Bacillus thuringiensis HD73 strain, A sigLmutant, HD(M-NM-^TsigL::kan), was constructed with insertion of kanamycin resistance gene cassete. We have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between mutant and wild-type strains. 2 ml samples were separately harvested from B. thuringiensis HD73 and HD(M-NM-^TsigL::kan) strains grown in SchaefferM-bM-^@M-^Ys sporulation medium (SSM) at stages T7 of stationary phase (7 hours after the end of the exponential phase). Three independent repeats were performed for each stain.
Project description:Transcriptional profiling of C. elegans nasp-1 / btr-1 mutant worms versus wild type N2 strain, both exposed to the bacterial pathogen Bacillus thuringiensis DB27. One-condition experiment. C. elegans nasp-1 / btr-1 mutant versus N2, exposed to Bacillus thuringiensis DB27. 3 biological replicates, including 1 dye-swaps.
Project description:This study generated CRISPR barcode sequencing data from a PyMT-Cas9 mammary tumor cell line engineered with integrated homing guide RNA (hgRNA) lineage barcodes. Cells were collected at day 5 and day 14 following doxycycline-induced Cas9 activation to characterize barcode mutation accumulation and lineage evolution. These data were used to evaluate LINEMAP, a computational framework for quantitative reconstruction of lineage topology and cell division history from evolving CRISPR barcodes.
Project description:Comparison at t2 (two hours into post-exponential phase growth as analyzed by OD measurements) of global expression profiles from a Bacillus thuringiensis 407 delta-sinI delta-sinR double gene deletion strain versus a Bacillus thuringiensis 407 delta-sinI single gene deletion strain, to analyze global expression changes following deletion of the sinR transcriptional regulator gene in a sinI-negative background.
Project description:To uncover, in an unbiased fashion, which elements of the 18 kb translocated region control EVI1 transcription, we devised a CRISPR/Cas9-based enhancer scanning approach. We considered all possible sgRNA target sites containing a canonical Cas9 PAM site (NGG) on both strands of the minimal 18 kb translocated region. Deep-sequencing libraries were generated by PCR amplification of sgRNA guide strands using primers that tag the product with standard Illumina adapters and a 4 bp sample barcode in a 2 step-PCR protocol.
Project description:Transcriptional profiling of C. elegans nasp-1 / btr-1 mutant worms versus wild type N2 strain, both exposed to the bacterial pathogen Bacillus thuringiensis DB27.
Project description:Transcriptional profiling of C. elegans young adult worms cultured on non-pathogenic Bacillus subtilis strain 67 versus age-matched worms cultured on the control lab food E. coli OP50. The goal was to identify genes regulated in response to differences in diet, which potentially confer immunity to later exposures to pathogenic Bacillus thuringiensis DB27.
Project description:Noncoding RNAs (ncRNAs) comprise an important class of natural regulators that mediate a vast array of biological processes, including the modulation of chromatin architecture. Moreover, artificial ncRNAs have revealed that the functional capabilities of RNA are extremely broad. To further investigate and harness these capabilities, we developed CRISPR-Display ("CRISP-Disp"), a targeted localization strategy that uses Cas9 to deploy large RNA cargos to specific DNA loci. We demonstrate that exogenous RNA domains can be functionally appended onto the CRISPR scaffold at multiple insertion points, allowing the construction of Cas9 complexes with RNAs nearing one kilobase in length, with structured RNAs, protein-binding cassettes, artificial aptamers and pools of random sequences. CRISP-Disp also allows the simultaneous multiplexing of disparate functions at multiple targets. We anticipate that this technology will provide a powerful method with which to ectopically localize functional RNAs and ribonuceloprotein complexes at specified genomic loci. RNA Immunoprecipitation (RIP) against FLAG-tagged Cas9 protein, coexpressed with a large pool of CRISPR RNAs bearing random internal insertions
