Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1010743 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3 was isolated from a system of alkaline soda lakes in the Kulunda Steppe. Its complete, circular genome was assembled from combined nanopore and illumina sequencing and its proteome was determined for three different experimental conditions: growth on Staphylococcus cells, casein, or peptone. AB-CW3 is an aerobic bacterium feeding mainly on proteins and peptides.
2020-11-03 | PXD021036 | Pride
Project description:Gan mice express Wnt1, Ptgs2, and Ptges, which develop inflammation-associated gastric tumors (Oshima et al, Gastroenterology 131: 1086, 2006). We examined the role of MyD88 in tumorigenesis by construction of Myd88-/- Gan mice and bone marrow transplantation into Gan mice from Myd88-/- mice. Total RNA was prepared from wild-type normal glandular stomach (n=3: WT 1âWT 3), B6 C2mE mice (n=3: C2mE 1âC2mE 3), B6 Gan mice (n=3: Gan1âGan3), B6 Gan MyD88-/- mice (n=3: Gan 1 (MyD88-/-)âGan 3 (MyD88-/-)), and B6 bone marrow transplanted Gan mice from Myd88-/- mice (n=3: BMT-Gan 1 (from MyD88-/-)âBMT-Gan 3 (from MyD88-/-)). We used Illumina HiSeq 2000, and examined expression profiles.
2015-12-15 | E-GEOD-70135 | biostudies-arrayexpress
Project description:Gan mice express Wnt1, Ptgs2, and Ptges, which develop inflammation-associated gastric tumors (Oshima et al, Gastroenterology 131: 1086, 2006). We examined the role of TNF-alpha in tumorigenesis by construction of TNF-/- Gan mice. We also examined genetic background difference in tumor phenotype by changing Gan mouse background from C57BL/6(B6) to BALB/c. Microarray analyses were performed to examine changes of expression profiles in tumors by TNF gene disruption or by changing genetic background. Total RNA was prepared from B6 Gan mice (n=3: Gan1-Gan3), B6-Gan TNF-/- mice (n=3: Gan(TNF KO)1-Gan(TNF KO)3), BALB-Gan mice (n=3: Gan(BALB/c)1-Gan(BALB/c)3), and wid-type normal glandular stomach (n=3: WT1-WT3). We used Affymetrix microarrays for hybridization, and examined expression profiles.
2012-12-27 | E-GEOD-43145 | biostudies-arrayexpress
Project description:Using an integrated model system for reproducible growth of biofilms, a JPIAMR-funded consortium of researchers* studied the expressed proteome of P. aeruginosa strain MPAO1 under i) planktonic growth, and ii) biofilm formation conditions. The model system included, as a first step, the sequencing and de novo assembly of the complete genome of this opportunistic human pathogen that belongs to the notorious group of Gram-negative ESKAPE pathogens. MPAO1 is also the parental strain for the widely used transposon (Tn) mutant library from the University of Washington. The complete MPAO1 genome sequence turned out to harbor several deletions and insertions compared to the PAO1-UW reference genome including numerous MPAO1-unique genes. As a second step in the model system, a biofilm flow cell based on poly (dimethylsiloxane) (PDMS) was designed to reproducibly study and identify known and novel genes related to biofilm growth and antibiotic resistance (ABR) from the Tn mutant collection. With the complete genome as optimal basis, publicly available TnSeq data were reanalyzed to identify known and novel essential genes. Furthermore, shotgun proteomics data was generated uncovering 1530 (planktonic) and 1728 (biofilm) expressed proteins, respectively, resulting in the identification of 1922 (33.1%) of the 5799 annotated P. aeruginosa MPAO1 proteins. They included proteins known to be differentially expressed during biofilm formation, and proteogenomic evidence for proteins uniquely encoded by MPAO1 as well as novel proteins.
2021-09-09 | PXD017122 | Pride
Project description:To develop a syngeneic mouse model of metastatic gastric cancer, we established the tumor organoids from gastric tumor arising in GAstric Neoplasia (GAN) mice (GAN-WT) which express Wnt1 and the PGE2 synthesis enzymes COX-2 and microsomal prostaglandin E synthase-1 (mPGES-1) in the stomach epithelium. Furthemore, GAN-WT organoids were genetically manupilated into p53 knockout organoids (GAN-p53KO) and KrasG12V-expressing GAN-p53KO organoids (GAN-KP).
2021-06-15 | GSE178087 | GEO
Project description:We have now developed an organoid-based model of gastric cancer from GAstric Neoplasia (GAN) mice, which express Wnt1 and the enzymes COX2 and microsomal prostaglandin E synthase 1 in the stomach. Both p53 knockout (GAN-p53KO) organoids and KRASG12V-expressing GAN-p53KO (GAN-KP) organoids were generated by genetic manipulation of GAN mouse–derived tumor (GAN-WT) organoids. To uncover the molecular mechanism underlying the intratumoral heterogeneity of GAN-KP tumors, we performed spatial transcriptomics analysis with the 10× Genomics Visium platform, which allows characterization of the spatial topography of gene expression.
2021-10-21 | GSE186290 | GEO
Project description:We applied RNA sequencing (RNA-seq) to study the gene expression profile in the liver of GAN DIO-NASH-HCC mice (non-tumorous tissue samples, n=9; tumor samples, n=9) and chow-fed controls (healthy liver samples, n=5)). Comparing tumour tissue of GAN DIO-NASH-HCC mice to healthy chow-fed controls, we find that tumors of GAN DIO-NASH-HCC mice show widespread regulations of genes associated with human HCC. Human HCC can be classified into three categories (S1-S3). Using the human S1-S3 gene classification described by Hoshida Y. et al. (2009), we find that GAN DIO-NASH-HCC tumors resemble the human S1 class of proliferating HCC tumors with poor prognosis.
2024-01-02 | GSE243976 | GEO
Project description:Janthinobacterium sp. 35 strain:35 Genome sequencing and assembly
| PRJNA402415 | ENA
Project description:RNA sequencing analysis of the transcriptome of V. parahaemolyticus RIMD2210633 strain grown under Zn-deficient (LB pretreated with 35 μM TPEN) and Zn-replete conditions (LB pretreated with 35 μM TPEN along with 500 μM Zn).
2022-04-24 | GSE200927 | GEO