Genome-wide baseline microRNA expression quantification in HapMap phase I CEU and YRI samples
ABSTRACT: Baseline microRNA (miRNA) expression was evaluated in 107 HapMap lymphoblastoid cell lines (LCLs; 53 CEU and 54 YRI) using Exiqon miRCURY LNA arrays v10.0 (Exiqon array). Total RNA from each of the 107 HapMap sample was labeled and hybridized onto an Exiqon array
Project description:Paired genomic DNA and cDNA samples obtained from lymphoblastoid cell lines from CEU and YRI HapMap individuals were hybridized to custom Illumina SNP arrays to study allele-specific expression in this tissue.
Project description:This SuperSeries is composed of the following subset Series: GSE23572: Custom array CGH validation of de novo CNVs in asthma samples GSE23575: Custom array CGH validation of de novo CNVs in CEU HapMap samples Refer to individual Series
Project description:The transcriptional response to heat shock is essential for cells to function effectively under stress. This is a highly heritable trait but the nature and extent of inter-individual variation in heat shock response are not well established. This dataset consists of the global transcription profiles for a panel of lymphoblastoid cell lines established from 60 founder individuals in the Yoruba HapMap population that have been exposed to heat shock. RNA was extracted from resting cells as well as cells that were exposed to heat shock at 42°C for 1 hour and then allowed to recover for 6 hours at 37°C. In combination with the HapMap genotypes for these individuals this enables the study of the effect of genetic variation on the heat shock response.
Project description:Expression of miRNAs in an EBV-positive B-cell strain, 28-2. 28-2 are infected with a derivative of the B-958 strain of EBV, which expresses eGFP constitutively and LMP1 fused to mRFP from its native promoter. Single cells were sorted by flow cytometry for their levels of LMP1-mRFP (5% expressing the lowest levels of LMP1-mRFP or 5% expressing the highest levels of LMP1-mRFP) Two-condition experiment: Low v. High LMP1-mRFP expression. Biological replicates: 3 Low LMP1-mRFP, 3 High LMP1-mRFP. Samples were normalized to the expression of miRNAs in a pool of unsorted 28-2 cells.
Project description:Lymphoblastoid cell lines (LCLs), originally collected as renewable sources of DNA, are now being used as a model system to study genotype-phenotype relationships in human cells. These cell lines have been used to search for genetic variants that are associated with drug response as well as with more basic cellular traits such as RNA levels. In setting out to extend such studies by searching for genetic variants contributing to drug response, we observed that phenotypes in LCLs were, in our lab and others, significantly affected by experimental confounders (i.e. in vitro growth rate, metabolic state, and relative levels of the Epstein-Barr virus used to transform the cells). As we did not find any SNPs associated with genome-wide significance to drug response, we evaluated whether incorporating RNA expression levels (and eQTLs) in the analysis could increase power to detect such effects. As previously shown, cis-acting eQTLs were detectable for a sizeable fraction of RNAs and baseline levels of many RNAs predicted response to several drugs. However, we found only limited evidence that SNPs influenced drug response through their effect on expression of RNA. Efforts to use LCLs to map genes underlying cellular traits will require great care to control experimental confounders, unbiased methods for integrating and interpreting such multi-dimensional data, and much larger sample sizes than have been applied to date. Experiment Overall Design: We studied 269 cell lines densely genotyped by the International HapMap Project . Cell lines were cultured and characterized at baseline for a variety of cellular phenotypes including growth rate, ATP levels, mitochondrial DNA copy number, EBV copy number, and measures of B-cell relevant cell surface receptors and cytokine levels. Each cell line was exposed in 384-well plates to a range of doses for each of seven drugs selected based on their divergent mechanisms of action and importance in clinical use for treatment of B-cell diseases, focusing on anti-cancer agents: 5-fluorouracil (5FU), methotrexate (MTX), simvastatin, SAHA, 6-mercaptopurine (6MP), rapamycin, and bortezomib. Drug response was measured using Celltiter Glo, an ATP-activated intracellular luminescent marker that, when compared to mock-treated control wells, can represent relative levels of cellular viability and metabolic activity. RNA was collected at baseline and RNA transcript levels were measured genome-wide on the Affymetrix platform. Baseline characterization and plating for drug response experiments was performed using batches of 90 cell lines from each HapMap analysis panel (CEU, JPT / CHB, and YRI) on each of three experiment days. The order of cell lines within each panel was randomized to avoid inducing artificial intra-familial correlation. Each drug was tested at a range of doses around the expected IC50 as reported for the drug by the NCI DTP; each dose of drug was tested in two wells per plate and on two separate plates. These replicate measurements for each cell line allowed assessment of intra-experimental variation. To evaluate day-to-day (i.e. inter-experimental) variation in all traits, a subset of 90 cell lines (30 from each of the three HapMap panels) was grown from a fresh aliquot and the entire experiment was repeated. To evaluate the effect of technical error on measured RNA levels, a set of 22 RNAs previously expression profiled (using Illumina HumanChip) at Wellcome Trust Sanger Institute (WTSI) (generously provided by Emmanouil T. Dermatsakis) was included in expression profiling at the Broad on Affymetrix arrays. Data can be downloaded from the Broad Institute web site: (http://www.broad.mit.edu/~yelensky/cell_lines_paper/). Please see Materials and Methods for details of QC, normalization, etc.
Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459. 12 samples were hybridized in each of the three pedigrees (36 samples total) against a previously well-characterized reference (GM15510; see Tuzun et al., Nat Genet 2005).
Project description:B lymphoblastoid cell lines were obtained from Coriell Cell Repositories. Cell lines were grown according to Coriell guidelines and total RNA was extracted, labeled, and hybridized to an Affymetrix Human Genome Focus Array as previously described. We found extensive variation in gene-expression levels and estimate that ~83% of genes are differentially expressed among individuals and that ~17% of genes are differentially expressed among populations. By decomposing total gene-expression variation into within- versus among-population components, we find that most expression variation is due to variation among individuals rather than among populations, which parallels observations of extant patterns of human genetic variation. Experiment Overall Design: We used microarrays to survey patterns of natural gene expression variation in 16 HapMap individuals derived from the CEU and YRI samples.
Project description:The abundance of miRNAs in Xenopus tropicalis embryos injected with a standard control morpholino oligo at early gastrula stage 13 was compared to that in sibling embryos in which the RNA binding proteins lin28a1, lin28a2 and lin28b have been knocked down by injection of translation blocking antisense morpholino oligos. A dual colour array system is used for analysis. n Expression levels are determined relative to a common, pooled mixed developmental stage RNA sample.
Project description:Comparison of non-coding RNA profiling by array in sublines of DU145 human prostate cancer cell lines created by in vivo cycling Cell lines created by removal and growth of metastatic human DU145 tumor cells from mouse lymph node (metastasized from prostate xenograft) for LN cells and extracted from lung after intravenous injection (ivLU cells). Cell line numebr represented number of in vivo cycles of metastatic selection Six condition experiment, individual cell line for each sample on array