Vector
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA315083 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide association studies for breast cancer have identified over 80 different risk regions in the genome, with the FGFR2 locus consistently identified as the most strongly associated locus. However, we know little about the mechanisms by which the FGFR2 locus mediates risk or the pathways in which multiple risk loci may combine to cause disease. Here we use a systems biology approach to elucidate the regulatory networks operating in breast cancer and examine the role of FGFR2 in mediating risk. Using model systems we identify FGFR2-regulated genes and, combining variant set enrichment and eQTL analysis, show that these are preferentially linked to breast cancer risk loci. Our results support the concept that cancer-risk associated genes cluster in pathways The data consists of 125 microarray samples from MCF-7 cells treated under different conditions, at 5 time points (0, 3, 6, 12 and 24 h) in order to perturb FGFR2 signalling by overexpressing the full length FGFR2b from a tetracycline-inducible expression vector. The data have been pre-processed in R using the beadarray package, and are presented in the form of log2 expression values. The experiment was carried out on 11 Humanv4 BeadChips using 12 samples per BeadChip. The original arrays contains 48324 features, with a mean of 22 beads per feature (Standard Deviation of 5)
2013-07-17 | E-GEOD-48927 | biostudies-arrayexpress
Project description:Hypoxia-regulated endothelial-specific lentiviral vector that can be used for endothelial-targeted gene therapy.
2021-08-12 | GSE151832 | GEO
Project description:Based on the hypothesis that, enhancing the local concentration of donor oligos could increase the correction rates, we generated and tested novel CRISPR-Cas9 systems, in which the DNA repair template is covalently conjugated to Cas9 (RNPD system). To validate our results from the HEK293T reporter cells, we here tested our approach at different endogenous genomic loci and in different cell types. We first targeted the human beta globin (HBB) locus in the K562 cell line, and analyzed correction- and editing frequencies using next generation sequencing (NGS). Next we targeted the Rosa26 and proprotein convertase subtilisin/kexin type 9 (Pcsk9) locus in mouse embryonic stem cells (mESCs). Here, RNPD system was always compared to Cas9 SNAP-tag fusion proteins with uncoupled donor oligos. To also directly compare the engineered RNPD system to the classical CRISPR-Cas9 system, we performed experiments where we used wild-type Cas9 with the uncoupled donor oligos as a control. We therefore targeted the fluorescent reporter locus as well as the endogenous loci HBB, empty spiracles homeobox 1 (EMX1), and C-X-C chemokine receptor type 4 (CXCR4) in HEK293T cells. Finally, we performed the analysis of three computationally predicted off-target sites of the reporter locus.
2018-06-04 | E-MTAB-6808 | biostudies-arrayexpress
Project description:Rhone_Prodelta_sediment Targeted Locus (Loci)
| PRJNA231894 | ENA