Similar Datasets
Project description:Reproducibility in molecular and cellular studies is fundamental to scientific discovery. To establish the reproducibility of a well-defined long-term neuronal differentiation protocol, we repeated the cellular and molecular comparison of the same two iPSC lines across five distinct laboratories. Despite uncovering acceptable variability within individual laboratories, we detect poor cross-site reproducibility of the differential gene expression signature between these two lines. Factor analysis identifies the laboratory as the largest source of variation along with several variation-inflating confounders such as passaging effects and progenitor storage. Single-cell transcriptomics shows substantial cellular heterogeneity underlying inter-laboratory variability and being responsible for biases in differential gene expression inference. Factor analysis-based normalization of the combined dataset can remove the nuisance technical effects, enabling the execution of robust hypothesis-generating studies. Our study shows that multi-center collaborations can expose systematic biases and identify critical factors to be standardized when publishing novel protocols, contributing to increased cross-site reproducibility.
| S-EPMC6178242 | biostudies-literature
Project description:Reproducibility in molecular and cellular studies is fundamental to scientific discovery. To establish the reproducibility of a well-defined long term neuronal differentiation protocol, we repeated the cellular and molecular comparison of the same two iPSC lines across five distinct laboratories. Despite uncovering acceptable variability within individual laboratories, we detect poor cross-site reproducibility of the differential gene expression signature between these two lines. Factor analysis identifies the laboratory as the largest source of variation along with several variation-inflating confounds such as passaging effects and progenitor storage. Single cell transcriptomics shows substantial cellular heterogeneity underlying inter-laboratory variability and being responsible for biases in differential gene expression inference. Factor analysis-based normalization of the combined dataset can remove the nuisance technical effects, enabling the execution of robust hypothesis generating studies. Our study shows that multi-center collaborations can expose systematic biases and identify critical factors to be standardized when publishing novel protocols, contributing to increased cross-site reproducibility.
2018-08-20 | GSE118733 | GEO
Project description:Reproducibility in molecular and cellular studies is fundamental to scientific discovery. To establish the reproducibility of a well-defined long term neuronal differentiation protocol, we repeated the cellular and molecular comparison of the same two iPSC lines across five distinct laboratories. Despite uncovering acceptable variability within individual laboratories, we detect poor cross-site reproducibility of the differential gene expression signature between these two lines. Factor analysis identifies the laboratory as the largest source of variation along with several variation-inflating confounds such as passaging effects and progenitor storage. Single cell transcriptomics shows substantial cellular heterogeneity underlying inter-laboratory variability and being responsible for biases in differential gene expression inference. Factor analysis-based normalization of the combined dataset can remove the nuisance technical effects, enabling the execution of robust hypothesis generating studies. Our study shows that multi-center collaborations can expose systematic biases and identify critical factors to be standardized when publishing novel protocols, contributing to increased cross-site reproducibility.
2018-08-20 | GSE118734 | GEO
Project description:Reproducibility of molecular phenotypes after long-term differentiation to Human iPSC-Derived Neurons: a multi-site omics study
| PRJNA486653 | ENA
Project description:Reproducibility of molecular phenotypes after long-term differentiation to Human iPSC-Derived Neurons: a multi-site omics study [bulk]
| PRJNA486654 | ENA
Project description:Reproducibility of molecular phenotypes after long-term differentiation to Human iPSC-Derived Neurons: a multi-site omics study [single-cell]
| PRJNA486655 | ENA
Project description:Live-cell imaging is crucial to appreciate the dynamics and the complexity of cellular interaction processes. However, live-cell imaging of human neurons is challenging due to neuronal sensitivity. Here, we describe a long-term live-cell imaging protocol for neurons derived from human induced pluripotent stem cells. By using an IncuCyte live-cell imaging system, we have obtained information on neuronal dynamics during the different stages of neurogenesis. The protocol has also been developed to monitor the dynamics of the neuronal intracellular organelles. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
| S-EPMC10665918 | biostudies-literature
Project description:The authors aimed to assess the reproducibility of normotension and white-coat, masked, and sustained hypertension in 839 untreated patients who underwent two separate assessments (median, 3; interquartile range, 0-13 months) by both office and ambulatory blood pressure (BP) monitoring (ABPM). The proportion of patients falling into the same category in the two assessments was: 52% normotension and 55% white-coat, 47% masked, and 82% sustained hypertension. The most frequent switch was to sustained hypertension (26% of white-coat and 33% of masked hypertension). No clinical factors predicted the change in category, except for higher office diastolic BP in patients with masked hypertension who developed sustained hypertension, compared with those who remained with masked hypertension (84±4 mm Hg vs 80±5 mm Hg; P=.006). The reproducibility of hypertension phenotypes was highly dependent on the time between assessments. The authors conclude that white-coat and masked hypertension phenotypes are only reproducible in the short-term, while they frequently shift towards sustained hypertension in the long-term.
| S-EPMC8032105 | biostudies-literature
Project description:The genetic architecture of non-small cell lung cancer (NSCLC) is relevant to smoking status. However, the genetic contribution of long-term smoking cessation to the prognosis of NSCLC patients remains largely unknown. We conducted a genome-wide association study primarily on the prognosis of 1299 NSCLC patients of long-term former smokers from independent discovery (n = 566) and validation (n = 733) sets, and used in-silico function prediction and multi-omics analysis to identify single nucleotide polymorphisms (SNPs) on prognostics with NSCLC. We further detected SNPs with at least moderate association strength on survival within each group of never, short-term former, long-term former, and current smokers, and compared their genetic similarity at the SNP, gene, expression quantitative trait loci (eQTL), enhancer, and pathway levels. We identified two SNPs, rs34211819TNS3 at 7p12.3 (P = 3.90 × 10-9) and rs1143149SEPT7 at 7p14.2 (P = 9.75 × 10-9), were significantly associated with survival of NSCLC patients who were long-term former smokers. Both SNPs had significant interaction effects with years of smoking cessation (rs34211819TNS3: Pinteraction = 8.0 × 10-4; rs1143149SEPT7: Pinteraction = 0.003). In addition, in silico function prediction and multi-omics analysis provided evidence that these QTLs were associated with survival. Moreover, comparison analysis found higher genetic similarity between long-term former smokers and never-smokers, compared to short-term former smokers or current smokers. Pathway enrichment analysis indicated a unique pattern among long-term former smokers that was related to immune pathways. This study provides important insights into the genetic architecture associated with long-term former smoking NSCLC.
| S-EPMC8128887 | biostudies-literature
Project description:ObjectiveQuantitative magnetic resonance imaging (MRI) evidence of mediobasal hypothalamic (MBH) gliosis positively correlates with body mass index (BMI) in adults. This has neither been well explored in children nor have other brain regions involved in appetitive processing been tested for evidence of gliosis.MethodsMulti-site cross-sectional study in children to test for differences in quantitative T2 signal (measure of gliosis) by region and to assess relationships with age and BMI. Participants underwent brain MRI using the same equipment and protocol to quantify T2 relaxation time in six bilateral regions of interest (ROIs): putamen, caudate, ventral striatum, amygdala, hippocampus and MBH, and three control regions: white matter, motor cortex and dorsal hypothalamus.ResultsThirty-one participants (61% female) were included in a combined sample from the University of Washington (N = 9) and John Hopkins University (N = 22). Mean age was 14 ± 3 years, and BMI z-score was 0.7 ± 1.1 (26% with obesity). No study site-related differences were seen in T2 relaxation time across all nine regions (chi2 (8): 9.46, P = .30). Regional differences in T2 relaxation time were present (P < .001). MBH presented longer T2 relaxation time, suggestive of gliosis, when compared to all regions (P < .001), including an intra-hypothalamic control. Physiological age-related declines in T2 relaxation times were found in grey matter ROIs, but not in the MBH (r = -0.14, P = .46). MBH was the only region with a positive correlation between T2 relaxation time and BMI z-score (r = 0.38, P = .03).ConclusionsIn a multi-site study, pilot data suggest that quantitative MRI detected normal maturation-related brain variation as well as evidence that MBH gliosis is associated with increased adiposity in children.
| S-EPMC8096323 | biostudies-literature