Lothian Birth Cohort 1921 whole genome sequencing study
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ABSTRACT:
PROVIDER: EGAS00001003818 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:1075 members of the Lothian Birth Cohort 1936 (LBC1936) were sequenced using the Illumina HiSeq X platform. The LBC1936 are a relatively healthy cohort of 1091 individuals who underwent cognitive and medical testing at a mean age of 69.5 (SD=0.8) years. They have since undergone four further waves of testing, approximately three years apart.
| EGAS00001003819 | EGA
Project description:297 members of the LBC1921 were sequenced using the Illumina HiSeq X platform. This dataset contains the gvcfs.
| EGAD00001006416 | EGA
Project description:297 members of the LBC1921 were sequenced using the Illumina HiSeq X platform. This dataset contains the fastq files.
| EGAD00001008775 | EGA
Project description:The repeatability of longitudinal measures of whole blood DNA methylation (obtained using the Illumina 450k chip) was assessed in two cohorts of ageing. The Lothian Birth Cohort of 1921 and the Lothian Birth Cohort of 1936. Data were collected at ages 70, 73, and 76 (LBC1936) and 79, 87, 90 (LBC1921) with 478 participants having two or more measures of methylation.
| EGAS00001000910 | EGA
Project description:GBS Sequencing Data from the same Australian rabbit population taken 16 years apart
| PRJEB36863 | ENA
Project description:Sleep deprivation (SD) in young adults is associated with metabolic, stress and cognitive responses that are also characteristic of brain aging. Given that sleep architecture changes with age, including increased fragmentation and decreased slow wave activity, it seems reasonable to investigate potential molecular relationships between SD and aging in brain tissue. Here, we tested the hypothesis that young rats exposed to 24 or 72 hour SD would respond with stress and aging-like shifts in brain hippocampal CA1 gene expression. SD animals showed blood corticosterone and weight changes consistent with a stress response. Microarray results, validated by Western blot and comparison to prior SD studies, pointed to disruptions in neurotransmission, sleep pressure signaling, and macromolecular synthesis. In a separate experiment, animals exposed to 24 or 72 hour novel environment stress recapitulated nearly one third of the SD transcriptional profile, particularly upregulated apoptotic and immune signaling pathways. Compared to aging (based on three previously published independent hippocampal aging studies), SD transcriptional profiles agreed for neurogenesis and energy pathways. However, immune signaling, glial activity, macromolecular synthesis and neuronal function all showed an SD profile that was, at least in part, opposed by aging. We conclude that while stress and SD have discrete molecular signatures, they do show a subset of highly similar changes. However, the same could not be said of aging and SD, where a similar subset of genes is changed, but in partially divergent directions. Finally, this work identifies presynaptic vesicular release and intercellular adhesion molecular signatures as novel targets for future SD-countering therapeutics. Subjects: Male Fischer 344 rats (3-5 months old, Harlan, Indianapolis): 37 in cohort 1 and 32 in cohort 2. Subjects were assigned to one of 5 treatment groups: Home Cage-HC n =17; 24 hour sleep deprivation- 24SD n = 16; 72 hour sleep deprivation- 72SD n = 20; 24 hour novel environment stress- 24NES n = 10; 72 hour novel environment stress- 72NES n = 6. Cohorts 1 and 2 were combined for microarray analyses. Sleep Deprivation: The multiple platform modification (Coenen and van Luijtelaar, 1985) of the classic 'flower pot' (Mendelson et al., 1974) technique in which animals are placed on an elevated platform over water was used. Pairs of SD animals (cage mates) were sleep deprived for 24 or 72 hours. Novel Environment Stress (NES): NES animals were exposed to a novel environment, but were not constrained from sleeping. These NES animals paralleled the sleep deprivation exposure duration (24 hour- n = 10, and 72 hour- n = 6). Tissue Isolation: On the day that animals were removed from the SD chambers, they were anesthetized with CO2 gas and decapitated. Brains were removed and immediately placed in oxygenated artificial cerebrospinal fluid (aCSF) containing (in mM) 114NaCl, 2.5 KCl, 2MgCl2, 30 NaHCO3, 10 Glucose and 2.2CaCl2. Hippocampi were dissected as described previously (Blalock et al., 2003; Kadish et al., 2009). Briefly, dissected hippocampi were immersed in 0C oxygenated aCSF and placed on a chilled glass petri dish. The CA1 region was dissected along the long axis of the hippocampus. CA1 tissue was flash frozen and stored at -80C until further use. Microarray Protocol: GCOS quality control measures of background signal (74.9 ± 2.1 cohort 1; 59.8 ± 2.3 cohort 2) and RawQ (2.3 ± 0.1 cohort 1; 1.9 ± 0.1 cohort 2), as well as a chip x chip correlation matrix of signal intensity data pointed to a global decrease in background signal intensity in Cohort 2. To control for this, each gene expression values for HC, 24SD and 72SD was standardized separately within cohort 1 and cohort 2, and then the two cohorts were combined. This retained the variability of each cohort, but removed the 'cohort effect' from the data. Pre-statistical filtering retained 'A' grade probe sets that were uniquely annotated (Affymetrix, June 2011) with gene symbols and had at least 6 presence calls across all 71 chips. This criterion was selected based on factorial analysis demonstrating < 5% probability of 6 or more chips being rated present for a given probe set by chance (Blalock, unpublished observations).
2012-07-16 | E-GEOD-34424 | biostudies-arrayexpress
Project description:0.6% Methamphetamine feeding experiments
| PRJNA117135 | ENA
Project description:LBC1921 and LBC1936 GVCFs called with GATK's HaplotypeCaller were combined and subject to variant quality score recalibration. This VCF contains the subset of samples (n = 296) from the LBC1921 cohort.
| EGAD00001005477 | EGA
Project description:Social play was performed on one cohort of adolescent rats. Other cohort was remaining naïve to behavioral testing. The rats were scarified following behavioral testing on postnatal day 38. Amygdala was isolated form the brain, homogenized the tissue, proteins were quantified, trypsin digested, and analyzed by LC ESI MS/MS.
2019-11-06 | PXD012677 | Pride