Project description:Time courses and RNA isolation. Strains were created that constitutively express fevR (FTT0383) transcript by replacing the endogenous fevR promoter with that of groES, and this gro::fevR region was integrated into either the wild-type, mglA mutant (GB2), or fevR knockout. Overnight cultures of F. novicida strains were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml. Samples were taken throughout the growth curve for RNA isolation and to determine the OD600. Four samples were taken during the growth curve at 2, 4, 6, and 8h for characterization of in gro::fevR bypass experiments. RNA was harvested and a common reference was created by combining equal amounts of RNA from each sample in the experiment. 1ug of RNA from either the samples or common reference was reverse transcribed and samples were labeled with Cy5 (samples) or Cy3 (reference) and hybridized to the Francisella microarray described in Brotcke, Weiss, et al. Infection and Immunity, 2006. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. all pairs
Project description:Time courses and RNA isolation. Strains were created that constitutively express fevR (FTT0383) transcript by replacing the endogenous fevR promoter with that of groES, and this gro::fevR region was integrated into either the wild-type, mglA mutant (GB2), or fevR knockout. Overnight cultures of F. novicida strains were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml. Samples were taken throughout the growth curve for RNA isolation and to determine the OD600. Four samples were taken during the growth curve at 2, 4, 6, and 8h for characterization of in gro::fevR bypass experiments. RNA was harvested and a common reference was created by combining equal amounts of RNA from each sample in the experiment. 1ug of RNA from either the samples or common reference was reverse transcribed and samples were labeled with Cy5 (samples) or Cy3 (reference) and hybridized to the Francisella microarray described in Brotcke, Weiss, et al. Infection and Immunity, 2006. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Project description:Time courses and RNA isolation. Overnight cultures of F. novicida strain U112, GB2, and fevR ko (383) were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml. Samples were taken throughout the growth curve for RNA isolation and to determine the OD600. Five samples were taken during the growth curve at 1, 3, 5, and 7.5h and 10h for characterization of single mutants or at 2, 4, 6, and 8h in gro::fevR bypass experiments. RNA was harvested and a common reference was created from each individual sample. 1ug of either the Sample, or Reference was reverse transcribed and labeled with either Cy5 (samples) or Cy3 (reference) and hybridized to a Francisella microarray previously described in Brotcke, Weiss, et al, Infection and Immunity, 2006. Groups of assays that are related as part of a time series. Age: Red channel represents 1ug of RNA from an individual timepoint Starting OD: Wt, GB2, and FTT0383 (fevR) ko were subbed to an OD of 0.01 in TSB + 0.2% cysteine in 200ml. Keywords: time_series_design Computed
Project description:Time courses and RNA isolation. Overnight cultures of F. novicida strain U112, GB2, and fevR ko (383) were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml. Samples were taken throughout the growth curve for RNA isolation and to determine the OD600. Five samples were taken during the growth curve at 1, 3, 5, and 7.5h and 10h for characterization of single mutants or at 2, 4, 6, and 8h in gro::fevR bypass experiments. RNA was harvested and a common reference was created from each individual sample. 1ug of either the Sample, or Reference was reverse transcribed and labeled with either Cy5 (samples) or Cy3 (reference) and hybridized to a Francisella microarray previously described in Brotcke, Weiss, et al, Infection and Immunity, 2006. Groups of assays that are related as part of a time series. Age: Red channel represents 1ug of RNA from an individual timepoint Starting OD: Wt, GB2, and FTT0383 (fevR) ko were subbed to an OD of 0.01 in TSB + 0.2% cysteine in 200ml. Keywords: time_series_design
2009-01-06 | GSE11554 | GEO
Project description:NDP gene mutations of FEVR patients
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:Understanding cancer immune escape is important to the comprehension of cancer development and to the development of cancer immunotherapy. We report here that ZNF408, encoded by a gene linked to familial exudative vitreoretinopathy (FEVR) and autosomal recessive retinitis pigmentosa (RP), is physically associated with the chromatin remodeler SETD1A/COMPASS complex in breast cancer cells. The ZNF408/SETD1A/COMPASS complex orchestrates the transcriptional activation of a cohort of genes via histone H3K4 trimethylation, particularly STING1 that are critically involved in innate immune response, leading to the release of multiple cytokines and activation of cytotoxic lymphocyte cells in tumor microenvironment. ZNF408 enhances STING expression and promotes anti-tumor immune responses both in vitro and in vivo. Importantly, the expression of ZNF408 is downregulated in breast carcinomas, and its level of expression is positively correlated with that of STING1 and negatively correlated with the histological grade of breast cancer. High ZNF408 is also correlated with high CD8+ T cell infiltration and favorable prognosis of breast cancer patients. Our study uncovers an important role for ZNF408 in innate immune response, supporting further investigations of the ZNF408-SETD1A/COMPASS-STING1 axis in cancer immune escape as well as in other ZNF408-associated diseases including FEVR and RP.
2024-06-26 | GSE254411 | GEO
Project description:Mutation of FZD4 gene in patients with FEVR
Project description:Here, we introduce a method termed DNA O-MAP, which uses programmable peroxidase-conjugated oligonucleotide probes to biotinylate nearby proteins. We show that DNA O-MAP can be coupled with sample multiplexed quantitative proteomics and next-generation sequencing to quantify DNA-protein and DNA-DNA interactions at specific genomic loci.