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ABSTRACT:
PROVIDER: PRJNA877851 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Overexpression of CIITA gene and overexpression and interference of AOX1
| PRJNA1261574 | ENA
Project description:Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate the activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector, cas1 deletion strain with csa3a overexpression vs. cas1 deletion strain carrying an empty expression vector, as well as interference-deficient strain with csa3a overexpression vs. interference-deficient strain carrying an empty expression vector. We find that cas genes (SiRe_0760, SiRe_0761, SiRe_0762, SiRe_0763), nucleotidyltransferase domain of DNA polymerase beta (SiRe_0459), chromosome segregation protein (SMC)-related ATPase (SiRe_0649), SMC-related protein (SiRe_1142) and three HerA helicases involved in DNA double break repair (encoded by SiRe_0064 and SiRe_0095 of nurA-herA operons, and SiRe_1857) were significantly up-regulated. Our data indicated that the Csa3a regulator couples transcriptional activation of spacer acquisition genes, CRISPR RNA transcription, DNA repair and genome stability genes.
2017-10-31 | GSE99099 | GEO
Project description:Resistance to proteasome inhibitors (PIs) is a ubiquitous clinical concern in multiple myeloma. We proposed that signaling-level responses after PI would reveal new means to enhance efficacy. Unbiased phosphoproteomics after the PI carfilzomib surprisingly demonstrated the most prominent phosphorylation changes on spliceosome components. Spliceosome modulation was invisible to RNA or protein abundance alone. Transcriptome analysis demonstrated broad-scale intron retention suggestive of PI-specific splicing interference. Direct spliceosome inhibition synergized with carfilzomib and showed potent anti-myeloma activity. Functional genomics and exome sequencing further supported the spliceosome as a specific vulnerability in myeloma. Our results propose splicing interference as an unrecognized modality of PI mechanism, reveal additional modes of spliceosome modulation, and suggest spliceosome targeting as a promising therapeutic strategy in myeloma.
2020-02-21 | PXD012172 | Pride
Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.
2021-02-20 | GSE167107 | GEO
Project description:<p>In this study, patients with advanced cancer across all histologies were enrolled in our IRB approved clinical sequencing program, called MI-ONCOSEQ, to go through an integrative sequencing which includes whole exome sequencing of the tumor and matched normal, and transcriptome sequencing. Four index cases were identified which harbor gene rearrangements of FGFR2 including two cholangiocarcinoma cases, a metastatic breast cancer case, and a metastatic prostate cancer case. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, including TCGA, we identified FGFR gene fusions with intact kinase domains of FGFR1, FGFR2, or FGFR3 in cholangiocarcinoma, breast cancer, prostate cancer, lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins in vitro induced cell proliferation, and bladder cancer cell lines that harbors FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types.</p>
| phs000602 | dbGaP
Project description:Purpose: Next generation sequencing (NGS) has revolutionized system-based analysis of cellular pathways. The goals of this study are to compare NGS-derived transcriptome profiling of human ovarian cancer cell, SKOV3 cells after endogenous overexpression of TNFAIP8L2 (TIPE2) . Methods: We constructed TIPE2 overexpression SKOV3 cell lines and control vector cell lines with lentivirus. Then the NGS based deep sequencing analysis was generated in triplicate to analyze the critical downstream targets after TIPE2 overexpression using ILLumina GAIIx. Results: The differentially expressed genes were identified using an optimized data analysis workflow, and we identified 49 upregulated and 28 downregulated genes in the SKOV3/TIPE2 group compared with the vector group using a |log2Foldchange|﹥0 and p < 0.05. Conclusions: Our study represents the first detailed analysis of transcriptomes in ovarian cancer cell line after overexpression of TIPE2 by RNA-seq technology.
2022-07-21 | GSE208351 | GEO
Project description:Whole RNA-sequencing analysis was performed by LC-Bio. Day-10 neurons from the Vector or circSCMH1 overexpression groups were collected in Trizol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimizes the interference of duplication generated by PCR amplification on the quantitative accuracy of transcriptome. RNA-seq reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was quantified as fragments per kilo base of exon per million fragments mapped (FPKM). Differentially expressed genes were determined by DESeq2 (DOI: 10.1186/s13059-014-0550-8).
2021-07-28 | GSE135121 | GEO