Similar Datasets
Project description:Many functions in host���microbiota interactions are potentially influenced by intestinal transit times, but little is known about the effects of altered transition times on the composition and functionality of gut microbiota. To analyze these effects, we cultivated the model community SIHUMIx in bioreactors in order to determine the effects of varying transit times (TT) on the community structure and function. After five days of continuous cultivation, we investigated the influence of different medium TT of 12 h, 24 h, and 48 h. For profiling the microbial community, we applied flow cytometric fingerprinting and revealed changes in the community structure of SIHUMIx during the change of TT, which were not associated with changes in species abundances. For pinpointing metabolic alterations, we applied metaproteomics and metabolomics and found, along with shortening the TT, a slight decrease in glycan biosynthesis, carbohydrate, and amino acid metabolism and, furthermore, a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate concentrations. Specifically, B. thetaiotaomicron was identified to be affected in terms of butyrate metabolism. However, communities could recover to the original state afterward. This study shows that SIHUMIx showed high structural stability when TT changed���even four-fold. Resistance values remained high, which suggests that TTs did not interfere with the structure of the community to a certain degree.
2020-02-06 | PXD017035 | Pride
Project description:To investigate how whether the RNAPII defect is premature pause release defect or gene body elongation defect due to splicing factor mutations, we peformed TT-TL-seq (TT seq with a time lapse component) in K562 cells (wild type and SF3B1K700E mutant; U2AF1wild type vs U2AF1 S34F mutant) at 4 days after mutant allele expression We then performed metaplot-based and gene expression analysis using data obtained from TT-TL seq
2024-03-12 | GSE225998 | GEO
Project description:The effects of gender-affirming testosterone therapy (TT) on breast cancer (BC) risk in the general trans masculine population and among BRCA1/2mut carriers are unclear. We found that TT reduced the size but not the number of terminal duct lobular units, increased stromal expression of estrogen receptor (ER), progesterone receptor, and Ki67, and had an immunosuppressive effect. We leveraged preclinical models to assess TT’s effect on BC incidence and biology. Consistent with the human data, TT reduced mouse mammary gland branching and the number of terminal end buds. TT decreased Pik3ca-related ER+ BC incidence by 81% compared to female controls (adj RR 0.19, 95% CI 0.08-0.45), but had no effect on Brca1-related triple negative BC incidence. Our findings clarify that TT modifies the risk for PIK3CA-related ER+ BC but not BRCA1-associated triple-negative BC, emphasizing the ongoing need for surveillance and individualized care in this population.
2025-09-15 | GSE306236 | GEO
Project description:We performed calibrated ChIP-seq, PRO-seq, TT-seq, or RNA-seq to investigate the role of protein phosphotase PNUTS-PP1 in regulating transcription. ChIP-seq, PRO-seq, TT-seq, or RNA-seq were normalizated by MEF as spike-in. The reads passed the quality check aligned to the human hg19 and mouse mm10 genome. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 3,12h, the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution.
2024-12-02 | GSE280548 | GEO
Project description:A large portion of the genome is transcribed but many of the resulting RNAs live only transiently and can generally not be mapped. Here we develop transient transcriptome sequencing (TT-Seq), a protocol that maps transcriptionally active regions in a nearly uniform manner and allows for unbiased monitoring of cellular RNA synthesis activity. Application of TT-Seq to human K562 cells recovers stable mRNAs and long intergenic non-coding RNAs, and additionally maps over 10,000 transient RNAs including enhancer RNAs, antisense RNAs, promoter-associated upstream antisense and convergent RNAs. TT-Seq also provides RNA half-lives, and reveals that transient RNAs are short and lack U1 motifs and secondary structure. TT-Seq further uncovers transcription termination sites and reveals a universal DNA motif for RNA polymerase II release.
2016-06-03 | GSE75792 | GEO
Project description:Reactive aldehydes such as 4-HNE, MDA and acrolein are implicated in the pathological development of diabetes as their widespread and universally exposed characteristics. Trans, trans-2,4-decadienal (tt-DDE) come from lipid peroxidation of omega-6 and is most abundant aldehyde in cooking oil fumes, while, its role in diabetes remained unknown. Aldh9a1 is a cytosolic enzyme that catalyze the NAD+-dependent oxidation of a variety of aldehydes and has its homology aldh9a1b in zebrafish. To investigate the function of endogenous and exogenous tt-DDE, aldh9a1b knockout zebrafish are established using CRISPR/Cas9 technology. TT-DDE was confirmed to act as substrate for aldh9a1b and a series of experiments are performed on a histological, metabolomic and transcriptomic level in aldh9a1b-/- zebrafish. Both aldh9a1b-/- larvae and adult fish displayed abnormal retinal vasculature and impaired glucose homeostasis, which are caused by tt-DDE induced downregulated insulin signaling pathway. Furthermore, the abnormal hyaloid vasculature in the fish can be reversed by insulin receptor sensitizer and metformin exhibited strongest effects among them. Altogether, these results identified tt-DDE as the preferred substrate for aldh9a1b, which subsequently causes microvascular damage and impaired glucose metabolism by insulin resistance.
2023-12-08 | GSE223340 | GEO
Project description:Global gene expression in TT cells treated with FAK inhibitors
2015-07-03 | GSE55619 | GEO
Project description:Thalassia testudinum Tt-101 Transcriptome - Tt-101-Leaf-3
| PRJNA696120 | ENA
Project description:Thalassia testudinum Tt-101 Transcriptome - Tt-101-Leaf-1
| PRJNA696118 | ENA