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Unknown,Transcriptomics,Genomics,Proteomics

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TGFÎ² signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Sander Hooff

PROVIDER: E-GEOD-79462 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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TGFÎ² signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [organoids]

Project description:The aim of this study was to determine the effects of TGFÎ² at the premalignant stage of CRC development. Organoid cultures were isolated from normal colon and from tubular adenomas. One normal colon culture was genetically engineered using the CRISPR-Cas9 system to carry the BRAFV600E mutation. Organoid cultures of three different tubular adenomas and two normal colon samples, and one BRAFV600E-mutant organoid culture received TGFÎ² or control treatment after which gene expression was analyzed by microarray (Affymetrix U133+ PM Genechip Array).

2016-06-01 | E-GEOD-79461 | biostudies-arrayexpress

TGFÎ² signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [adenomas]

Project description:Colorectal cancer can be divided into four consensus molecular subtypes, which might associate with distinct precursor lesions. The aim of this study was to determine the subtype affiliation of two types of colorectal adenomas: tubular adenomas (TAs) and sessile serrated adenomas (SSAs) and to determine the activity of TGFÎ² signaling and the role of this cytokine in subtype affiliation. Adenoma samples were collected in the Academic Medical Center (AMC), Amsterdam, The Netherlands. Tubular adenomas (TAs) were obtained from familial adenomatous polyposis (FAP) patients and sessile serrated adenomas (SSAs) were collected from serrated polyposis syndrome (SPS) patients. Gene expression was analyzed for 7 sessile serrated adenomas (SSA) and 9 tubular adenomas (TA).

2016-06-01 | E-GEOD-79460 | biostudies-arrayexpress

miR-200 overexpression in colorectal cancer lines

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Effect of high-dose epinephrine on myocardial gene set expression

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2023-05-31 | E-MTAB-13031 | biostudies-arrayexpress

bulkRNA seq of spleens from humanized mice comparing NRG to NSG-DKO strains and additionally vaccination using lentiviral constructs

Project description:Decifering why NSG-DKO mice have better humanization upon CD34+ stem cell injection than NRG mice. Additionally, checking effects of lentivirus administration that delivers human HLAs, human cytokines and a viral antigen, which, as a consequence, should improve human adaptive immunity in our huNSG-DKO mouse model.

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2024-03-12 | E-MTAB-13832 | biostudies-arrayexpress

Effect of 20-Hete and dietary restriction on murine kidneys

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2022-05-10 | E-MTAB-11428 | biostudies-arrayexpress

Evidence for long-distance trade in exotic foods and spices from South Asia to the Near East in the 2nd millennium BCE

Project description:Although the key role of long-distance trade in the transformation of cuisines worldwide has been well-documented since at least the Roman era, the prehistory of the Eurasian food trade is less visible. In order to shed light on the transformation of Eastern Mediterranean cuisines during the Bronze and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the 2nd millennium BCE in the Southern Levant. Our results provide clear evidence for the consumption of expected staple foods, such as cereals (Triticeae), sesame (Sesamum) and dates (Phoenix). We additionally report evidence for the consumption of soybean (Glycine), probable banana (Musa), and turmeric (Curcuma), which pushes back the earliest known availability of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early 2nd millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such trade goods likely reached the Eastern Mediterranean in the form of oils, dried fruits, and spices. These novel insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age and also the degree of globalization in early Eastern Mediterranean cuisine.

2020-12-22 | PXD021498 | Pride

A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth

Project description:To investigate the downstream effects of a polymorphism in the pyk1 gene of Schizosaccharomyces pombe (A343T) we generated a strain that differed from the lab strain (JB50) only in the amino acid at position 343 of pyk1 where a threonine was substituted with an alanine. Five replicates were grown for each strain and harvested in log phase. From each of these cultures RNA was isolated and underwent polyA-enrichment. Reads were sequenced and mapped against the strain-specific genomes.

2020-06-08 | E-MTAB-8847 | biostudies-arrayexpress

Relief Food Subsistence Revealed by Microparticle and Proteomics Analyses of Dental Calculus From Victims of the Great Irish Famine

Project description:Food and diet were class markers in nineteenth-century Ireland, which became evident as nearly one million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845–1852. Famine took hold after a blight (Phytophthora infestans) destroyed the only means of subsistence—the potato crop—for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid-nineteenth-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the Famine. The sample derives from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52°39’N, -7°15’W). The results corroborate the historical accounts of food provisions before and during the Famine, with evidence of corn (maize), potato and cereal starch granules from the microparticle analysis and milk proteins from the proteomic analysis. Unexpectedly, there is also evidence of egg proteins—a food source generally reserved only for export and the better-off social classes—which highlights the variability of the Famine experience for those who died. Through historical contextualisation, this study shows how the notoriously monotonous potato diet of the nineteenth-century Irish poor was supplemented by other foodstuffs on an opportunistic basis. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability.

2019-10-17 | PXD015002 | Pride

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