Genetic and genomic stability across lymphoblastoid cell line expansions
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PROVIDER: PRJNA480126 | ENA |
REPOSITORIES: ENA
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Project description:Genetic and genomic stability across lymphoblastoid cell line expansions
| PRJNA480125 | ENA
Project description:OBJECTIVE:Lymphoblastoid cell lines are widely used in genetic and genomic studies. Previous work has characterized variant stability in transformed culture and across culture passages. Our objective was to extend this work to evaluate single nucleotide polymorphism and structural variation across cell line expansions, which are commonly used in biorepository distribution. Our study used DNA and cell lines sampled from six research participants. We assayed genome-wide genetic variants and inferred structural variants for DNA extracted from blood, from transformed cell cultures, and from three generations of expansions. RESULTS:Single nucleotide variation was stable between DNA and expanded cell lines (ranging from 99.90 to 99.98% concordance). Structural variation was less consistent across expansions (median 33% concordance) with a noticeable decrease in later expansions. In summary, we demonstrate consistency between SNPs assayed from whole blood DNA and LCL DNA; however, more caution should be taken in using LCL DNA to study structural variation.
| S-EPMC6076395 | biostudies-literature
Project description:AHR ChIP-seq in lymphoblastoid cell line
| PRJNA479757 | ENA
Project description:RNA-seq was used to characterize the LMP1 mediated regulation of host target gene regulation. We knocked out LMP1 in GM12878 Lymphoblastoid cell line (LCL). The GM12878 LCL expressing control sgRNA was used as the control.
2023-04-25 | GSE228167 | GEO
Project description:Transcriptome analysis for LMP1 depletion in GM12878 Lymphoblastoid cell line (LCL)
| PRJNA948425 | ENA
Project description:The data describe longitudinal profiling, pre and post treatment of a human B lymphoblastoid cell line (B-LCL). The cells were treated with Everolimus at timepoint 7 and the full untargeted proteomics and transcriptomics were profiled over a total of 24 timepoints (over 12 hours), with samples acquired once every half-hour. A validation experiment was repeated as a separate experiment using a subset of the time points.
2017-06-19 | MSV000081170 | MassIVE
Project description:ChIP-seq was done on one lymphoblastoid cell lines for vehicle control, or 3-MC agonist treatment to identify AHR binding regions throughout the genome. We identified 17,688 common binding peaks between all ChIP treatments
2018-07-06 | GSE116632 | GEO
Project description:Clostridium difficile genomic stability
| PRJEB2195 | ENA
Project description:Transcript abundance results from the balance between transcription and mRNA decay, and varies pervasively in humans. We have examined the effect of DNA variation on mRNA half-life differences by conducting a genome-wide survey of mRNA stability in seven human HapMap lymphoblastoid cell lines (LCLs). We determined the mRNA half-life for each gene from the ratio of 4-thio-uridine (4sU)-labeled nascent RNAs to total RNAs. 5,145 (46%) of 11,132 analyzed genes showed inter-individual mRNA half-life differences at a false discovery rate, FDR<0.05. As previously reported, we found transcription to be the main factor influencing transcript abundance. Although mRNA half-life explained only ~6% of transcript abundance on average, it explained ~16% for the subset of genes (~10%) showing inter-individual mRNA half-life differences (P<0.001). We confirmed previously reported correlations of mRNA half-life with transcript length, 3’-UTR length, and number of exon-junctions per kb of transcript. The number of miRNA targets in 3’-UTRs was negatively correlated with half-life (P=2.2×10-16), a new observation that is consistent with the role of miRNA in inducing mRNA degradation. Notably, coding GC and GC3 content showed positive correlations with mRNA half-life in genes with inter-individual mRNA half-life differences, implying a role of mRNA stability in shaping synonymous codon usage bias. Consistently, G or C alleles of coding SNPs were found associated with longer mRNA half-life (P=0.021). As expected, we also found that nonsense SNPs were associated with shorter mRNA half-life (P=0.009). Our results strongly suggest that inter-individual mRNA stability differences are widespread and affected by DNA sequence and composition variation.
2013-01-01 | GSE34204 | GEO
Project description:Many aged individuals develop monoclonal expansions of CD8 T cells. These expansions are derived from a CD8 memory T cell that outcompetes neighboring CD8 T cells. The molecular alterations within clonal expansions that confer this competitive advantage relative to other CD8 T cells remains unknown. These microarray experiments were designed to identify genes differentially expressed in age-associated expansions of CD8 memory T cells relative to polyclonal CD8 memory T cells found in the same aged mice. Subsequent analysis of these data identified two major types of clonal expansions, distinguished by expression level of integrin a4 mRNA and protein. Based on this classification, Expansion_rep1 belongs to the integrin a4 high subtype of clonal expansions. In contrast, reps 2, 4, and 5 belong to the integrin a4 low subtype of clonal expansions. Given the divergent biological properties of these two subtypes of clonal expansions, we have focused genes differentially expressed between Expansion_rep 2, 4, and 5 and their paired PolyclonalAged samples. Experiment Overall Design: A total of 8 samples were analyzed for gene expression using the Affymetrix mouse genome 430 2.0 microarray platform. The experimental samples of interest were age-associated clonal expansions of CD8 memory T cells. We purified four clonal expansions from four independent, aged mice (indicated as "Expansion" rep1 2, 3, 4). For each clonal expansion of CD8 memory T cells that was purified, there was a paired control in which polyclonal CD8 memory T cells were harvested from the same aged mouse (denoted as "PolyclonalAged" rep1, 2, 3, 4). These paired samples allow one to consider gene expression changes from mice which have undergone the same age-associated changes in biology. The predominant comparison this study focused on was changes in gene expression between age-associated clonal expansions of CD8 memory T cells and their paired, polyclonal CD8 memory T cells. A total of 4 of these pairs were collected.
2008-10-25 | E-GEOD-11677 | biostudies-arrayexpress