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Integrated Exome-seq analysis of tumor thrombus

ABSTRACT: We prospectively enrolled 83 patients with a renal mass and TT scheduled to undergo surgical resection. To accurately integrate genomic and transcriptomic findings and enable histological co-registration, simultaneous isolation of DNA and RNA was performed from individual samples characterized histologically through immediately flanking sections

PROVIDER: EGAS00001005511 | EGA |

REPOSITORIES: EGA

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Integrated RNA-seq analysis of tumor thrombus

Project description:We prospectively enrolled 83 patients with a renal mass and TT scheduled to undergo surgical resection. To accurately integrate genomic and transcriptomic findings and enable histological co-registration, simultaneous isolation of DNA and RNA was performed from individual samples characterized histologically through immediately flanking sections

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Simultaneous Integrated Boost Preoperative Radiotherapy for Rectum Cancer

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Simplified Human Intestinal Microbiota (SIHUMIx) LC-MS/MS dataset

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:tt

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Sugarcane_flanking

Project description:Transgenic sugarcane flanking sequences

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Hox Abdominal-B Genes in the Developing Kidney

Project description:The Hox complex consists of 39 genes arranged in 4 clusters of flanking genes and 13 paralogous groups in mammals. To assess the functional redundancy of Hox abdominal-B genes during renal development, we used a modified recombineering strategy to simultaneous introduce frameshift mutations into the Hox9, Hox10, and Hox11 flanking genes of the HoxA, HoxC, and HoxD paralogous groups. We performed RNA seq on whole kidneys at E18.5 in triplicates for representative genotypes including: wild type; Hoxa9,10,11-/- HoxC9,10,11+/-, Hoxa9,10,11+/- HoxC9,10,11-/-, Hoxa9,10,11-/- HoxC9,10,11-/-. Our results suggest that the loss of Hox function results in a partial metanephric to mesonephric transformation, with tubules co-expressing markers of both proximal tubules and collecting ducts, as well as markers of mesonephric-derived epididymis tubules.

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [TT-TL seq]

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

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The INTEGRATE project

Project description:The INTEGRATE project

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