Project description:Investigation of lung adenocarcinoma (LUAD) and breast cancer cells cultured in either a nutrient-rich or -restricted culture conditions trough a multi-omics approach, including transcriptomics, to explore the molecular changes underlying the transition from 2D to 3D cultures.
2023-04-05 | GSE215235 | GEO
Project description:Bacterial communities of water in V-trough
Project description:Signaling trough cytoplasmic or nuclear action of p53 is a major response mechanism to cellular stresses. Here we perform transcriptomics after p53 re-expression on a CRISPR/Cas9 knock out background to reveal a distinct starvation-specific transcriptome response and novel nutrient-dependent p53 target genes.
Project description:Trough a two components inducible system, we expressed ectopically in the SAM a resistant version of AP2 to the regulation of miR172 (AP2m3). The differentially expressed genes by AP2 induction allows the identification of differents groups of genes that could mediate AP2 functions in the SAM.
Project description:Confluent U2OS cells were released to serum-free medium, and continued to grow for 36 h (Per2-dLuc peak) or 48 h (Per2-dLuc trough), then added DRB (10uM) treatment for 0.5, 1.5, 3.5 h, then added BrU (250uM) for 0.5 h, harvested total RNA, captured with anti-BrU antibody, and conduced hi-seq.
Project description:Sequencing files provided here are mouse liver DNase-seq for male mouse livers collected at either a peak or trough of GH/STAT5 activity. This is part of a larger study that includes DNase-seq in mouse liver from hypophysectomized males, females, and hypox-male mice given a single dose of GH. DNase hypersensitivity site (DHS) analysis of these livers established that the naturally occurring, endogenous male rhythm of plasma GH pulse-stimulated liver STAT5 activation induces dynamic, repeated cycles of chromatin opening and closing at several thousand liver DHS and comprises a novel mechanism conferring male bias to liver chromatin accessibility.
2023-08-21 | GSE131848 | GEO
Project description:Protist diversity in the Okinawa Trough and Kuroshio Current
Project description:Tacrolimus (TAC) is an immunosuppressant widely used in kidney transplantation. TAC displays considerable inter-individual variability in pharmacokinetics (PK). Genetic and clinical factors play important roles in TAC PK. To define genetic factors associated with tacrolimus blood trough concentration, we performed a genome-wide association study of renal transplant samples from 251 Chinese renal transplant recipients. We identified 23 single nucleotide polymorphisms (SNPs) related to TAC PK variability. All 23 genome-wide significant SNPs (p<5E-8) were located on chromosome 7, including rs776746. These findings suggest that these SNPs may be associated with the unexlained TAC PK variability in renal transplant recipients and require further investigation.
Project description:To understand the transcriptional basis of circadian rhythms in mouse liver, we generated genome-wide profiles of RNA polymerase II (Pol 2) DNA occupancy and the histone modifications H3K4me3 and H3K36me3 around the circadian cycle. We found that Pol 2 occupancy at promoters and in gene bodies cycle in synchrony, suggesting that Pol 2 recruitment at promoters underlies circadian gene transcription. On average, Pol 2 occupancy precedes mRNA accumulation by about three hours. Promoters of transcribed genes have tri-methylated H3K4 residues even at their trough activity times, and the tri-methylation levels increase in phase with Pol 2 loading. In contrast, the tri-methylation of H3K36 residues lags transcription by three hours with amplitudes that are markedly shallower, indicating that this mark is less dynamic on the circadian time scale. The comparison of Pol 2 occupancy and mRNA accumulation revealed that both transcriptional and post-transcriptional regulatory mechanisms can account for diurnal mRNA profiles. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/ Contributed by members of CycliX consortium (http://cyclix.vital-it.ch/) 28 samples examinded, 7 Polr2b, 7 H3K4me3, 7 H3k36me3, 7 input samples.
