Ena-DATASET-ICR-PTGT-15-10-2018-17:54:40:362-3 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001004396 | EGA |
REPOSITORIES: EGA
Publications
Rare disruptive mutations and their contribution to the heritable risk of colorectal cancer.
Chubb Daniel D Broderick Peter P Dobbins Sara E SE Frampton Matthew M Kinnersley Ben B Penegar Steven S Price Amy A Ma Yussanne P YP Sherborne Amy L AL Palles Claire C Timofeeva Maria N MN Bishop D Timothy DT Dunlop Malcolm G MG Tomlinson Ian I Houlston Richard S RS
Nature communications 20160622
Colorectal cancer (CRC) displays a complex pattern of inheritance. It is postulated that much of the missing heritability of CRC is enshrined in high-impact rare alleles, which are mechanistically and clinically important. In this study, we assay the impact of rare germline mutations on CRC, analysing high-coverage exome sequencing data on 1,006 early-onset familial CRC cases and 1,609 healthy controls, with additional sequencing and array data on up to 5,552 cases and 6,792 controls. We identif ...[more]
Similar Datasets
Project description:ChIP-seq data (H3K4Me3, H3K27Ac histone modifications) of Hodgkin lymphoma cell line L-428. Samples were processed as previously described (Sud et al., 2018). The files are in bam format, aligned to build 37 of the human genome.
| EGAD00001004322 | EGA
Project description:In situ promoter capture Hi-C on Hodgkin lymphoma cell line L-428 in experimental triplicates. Hi-C libraries were prepared as previously described (Orlando et al., 2018, https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cphg.63). Promoter capture was based on 32,313 biotinylated 120-mer RNA baits (Agilent). Hi-C libraries were sequenced using Illumina HiSeq 2000 technology. The files are in FASTQ format.
| EGAD00001004321 | EGA
Project description:BackgroundCurrently available infant body composition measurement methods are impractical for routine clinical use. The study developed anthropometric equations (AEs) to estimate fat mass (FM, kg) during the first year using air displacement plethysmography (PEA POD® Infant Body Composition System) and Infant quantitative magnetic resonance (Infant-QMR) as criterion methods.MethodsMulti-ethnic full-term infants (n = 191) were measured at 3 days, 15 and 54 weeks. Sex, race/ethnicity, gestational age, age (days), weight-kg (W), length-cm (L), head circumferences-cm (HC), skinfold thicknesses mm [triceps (TRI), thigh (THI), subscapular (SCP), and iliac (IL)], and FM by PEA POD® and Infant-QMR were collected. Stepwise linear regression determined the model that best predicted FM.ResultsWeight, length, head circumference, and skinfolds of triceps, thigh, and subscapular, but not iliac, significantly predicted FM throughout infancy in both the Infant-QMR and PEA POD models. Sex had an interaction effect at 3 days and 15 weeks for both the models. The coefficient of determination [R2 ] and root mean square error were 0.87 (66 g) at 3 days, 0.92 (153 g) at 15 weeks, and 0.82 (278 g) at 54 weeks for the Infant-QMR models; 0.77 (80 g) at 3 days and 0.82 (195 g) at 15 weeks for the PEA POD models respectively.ConclusionsBoth PEA POD and Infant-QMR derived models predict FM using skinfolds, weight, head circumference, and length with acceptable R2 and residual patterns.
| S-EPMC8821135 | biostudies-literature
Project description:Whole genome sequencing reads consisting of paired end Fastq and aligned bam files from pediatric medulloblastoma samples.
| EGAD00001004115 | EGA
Project description:Genomic, proteomic, and metabolomic technologies continue to receive increasing interest from environmental toxicologists. This interest is due to the great potential of these technologies to identify detailed modes of action and to provide assistance in the evaluation of a contaminant?s risk to aquatic organisms. Our experimental model is the zebrafish (Danio rerio) exposed to reference endocrine disrupting compounds in order to investigate compound-induced changes in gene transcript profiles. Adult, female zebrafish were exposed to 0, 15, 40, and 100 ng/L of 17 alpha-ethynylestradiol (EE2) and concentration and time-dependent changes in hepatic gene expression were examined using Affymetrix GeneChip® Zebrafish Genome Microarrays. At 24, 48, and 168 hours, fish were sacrificed and liver mRNA was extracted for gene expression analysis (24 and 168 hours only). In an effort to link gene expression changes to effects on higher levels of biological organization, body and ovary weights were measured and blood was collected for measurement of plasma steroid hormones (17 beta-estradiol (E2), testosterone (T)) and vitellogenin (VTG) using ELISA. EE2 exposure significantly affected GSI, E2, T, VTG and gene expression. We observed 1575 genes that were significantly affected (up- or down-regulated by at least 1.5-fold (p ? 0.001) in a concentration-dependent manner by EE2 exposure at either 24 or 168 hours. EE2 exposure altered transcription of genes involved in steroid hormone homeostasis, cholesterol homeostasis, retinoic acid metabolism, and cell growth and proliferation. Plasma VTG was significantly increased at 24, 48, and 168 hours (p<0.05) at 40 and 100 ng/L and at 15 ng/L at 168 hours. E2 and T were significantly reduced following EE2 exposure at 48 and 168 hours. GSI was decreased in a dose-dependent manner at 168 hours. In this study, we identified genes involved in a variety of biological functions that have the potential to be used as markers of exposure to estrogenic substances. Future work will evaluate the use of these genes in zebrafish exposed to weak estrogens to determine if these genes are indicative of exposure to estrogens with varying potencies.
2007-02-24 | E-TABM-105 | biostudies-arrayexpress
Project description:This dataset contains variant call format files generated from whole exome sequencing of germline DNA from indiviudals with diagnosed with testicualr germ cell cancer.
| EGAD00001004345 | EGA
Project description:ChIP-Seq - CEBPE - REH. The ETV6/RUNX1 translocated acute lymphoblastic leukaemia cell line.
REH was used to perform ChIP-Seq using a CEBPE antibody. Cells were fixed in 1% formaldehyde for 10mins, prior to preparation of chromatin using Active Motif Express ChIP-IT. 2ug of antibody (anti CEBPE Atlas Antibodies HPA002928)was added to 25ug of chromatin O/N at 4C with rotation. Duplicate reactions were pooled and purified. 10ng of ChIP’d and input DNA used for Illumina NGS preparation (NEBNext ChIP-Seq Library kit; New England Biolabs), CEBPE and Input DNA ChIP samples were sequenced on a MiSeq using 150bp Kit v3 paired end and a HiSeq 2500 using 2x101 version 4 paired end (Illumina) respectively. Reactions performed in duplicate.
shCEBPE RNA-Seq - REH.
REH cells were lentivirally transduced with a pTRIPZ shRNA vector for transcriptional profiling of CEBPE. Two controls (empty and non-targeting) and two CEBPE shRNAs (V3THS_150517(A13), V3THS_404312(G3) Dharmacon, GE) were transduced into REH cells. Cells were treated with 1ug/ml doxycyclin for 144hrs and total RNA purified using Qiagen RNeasy. Knock down of CEBPE was validated by qRT. RNA integrity >7.7 for all samples. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illuimna HiSeq 2500 using 2x101 version 4 paired end chemistry. 3 biological replicates of each samples were prepared.
| EGAD00001004084 | EGA
Project description:BackgroundMost countries worldwide, especially low- and middle-income countries (LMICs), are facing an increasing prevalence of fast-food consumption and multiple burdens of malnutrition among young adolescents.ObjectiveTo compare the prevalence of fast-food consumption among young adolescents in LMICs.MethodsWe used data from the most recent Global School-Based Student Health Survey (2009-2015), which had been collected using a standardized questionnaire. The weighted prevalence and 95% confidential intervals of fast-food consumption were calculated overall and in subgroups stratified by age, sex, and nutritional status. The pooled overall and regional estimates were obtained using a random-effects model. Heterogeneity was assessed using the I2 statistic. The associated risk factors for fast-food consumption were explored using logistic regression analysis.ResultsOur study comprised 153,496 young adolescents (46.90% boys) from 54 LMICs. Overall, approximately 55.2% (51.3-59.1%) of the adolescents consumed fast food at least 1 day per week, and 10.3% (8.3-12.4%) did so 4-7 days per week. The prevalence of fast-food consumption 4-7 days per week was lowest in the Americas (8.3%; 6.7-9.9%) and highest in Southeast Asia (17.7%; 2.3-33.2%). At a country level, the prevalence was lowest in Pakistan (1.5%; 1.0-2.0%) and highest in Thailand (43.3%; 40.4-46.1%). Furthermore, in subgroups stratified by nutritional status, the prevalence was lowest in the obesity group (6.6%; 4.5-8.7%). Factors such as age, sex, BMI, food insecurity, fruit consumption, vegetable consumption, soft-drink consumption, smoking, physical activity level, and sedentary behavior level were found to be correlated with fast-food consumption.ConclusionsThe identified high prevalence of fast-food consumption among young adolescents in LMICs indicates the urgent need to prioritize the implementation of healthy-diet promotion programs to improve adolescent health in these countries.
| S-EPMC7480506 | biostudies-literature
Project description:Sex differences in episodic memory have been reported. We investigate (1) the existence of sex differences in verbal and other episodic memory tasks in 54 countries, and (2) the association between the time- and country-specific social progress indicators (a) female to male ratio in education and labor force participation, (b) population education and employment, and (c) GDP per capita, and magnitude of sex differences in verbal episodic memory tasks. Data were retrieved from 612 studies, published 1973-2013. Results showed that females outperformed (Cohen's d > 0) males in verbal (42 out of 45 countries) and other (28 out of 45 countries) episodic memory tasks. Although all three social progress indicators were, separately, positively associated with the female advantage in verbal episodic memory performance, only population education and employment remained significant when considering the social indicators together. Results suggest that women's verbal episodic memory performance benefits more than men's from education and employment.
| S-EPMC6476491 | biostudies-literature