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Quantitative Analysis of Wild Type CBL, CBL 70Z and Y371S 3T3 Stable Cell Transcriptomes

ABSTRACT: Quantitative Analysis of Wild Type CBL, CBL 70Z and Y371S 3T3 Stable Cell Transcriptomes

PROVIDER: PRJNA495948 | ENA |

REPOSITORIES: ENA

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Quantitative Analysis of Wild Type CBL, CBL 70Z and Y371S 3T3 Stable Cell Transcriptomes

Project description:Cbl (Casitas B-lineage lymphoma) is a prominent post-translational regulator of protein tyrosine kinases (PTKs) that targets activated receptors for ubiquitination-mediated degradation. However, mutations within its E3 ubiquitin ligase activity rendering RING domain are often not sufficient to induce transformation. Rather, a conserved residue (Y371) within the linker helix region (LHR) of Cbl has been a mutational hotspot in myeloproliferative diseases. Interestingly, phosphorylation of Y371 is a prerequisite for Cbl’s ability to ubiquitinate PTKs. We have previously shown that Y371 mutations affect the conformation of Cbl that can be related to its transformation potential. We wanted to investigate for any additional advantage that the Cbl-Y371 mutants could gain over their wild-type counterpart so as to explain their oncogenicity. In our current study, we wanted to investigate the transcriptome profiles of cells overexpressing WT CBL or CBL-70Z, a well-characterized oncogenic CBL mutant lacking residues 366-382 and Y371S a prevalent MDS/MPN CBL mutant. We found an interesting inverse correlationship between the transcriptome of cells expressing WT CBL and the mutant CBLs. The results from this study can be linked to the oncogenic abilities of the mutant CBLs.

2019-10-20 | GSE121176 | GEO

Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 3T3 cell transcriptomes

Project description:Purpose: The goals of this study were to compare gene expression profiles of mouse NIH/3T3 cells with intact or disrupted Mki67 gene. Methods: mRNA profiles of wild-type (WT) and two clones of Ki-67 knockout (Mki67−/−) mouse NIH/3T3 cells, all in duplicate, were generated by deep sequencing using Illumina Hiseq2500 in single-end read mode, 50bp. The sequence reads that passed quality filters were aligned to the mouse genome, quantified, and differential gene expression (DGE) analysis was performed using DEseq2. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (GRCm38.p6) and identified differentially expressed genes. This revealed widespread changes in gene expression, with 2558 genes significantly deregulated in independent clones of Mki67-/- cells (q < 0.05) Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2021-02-18 | GSE162352 | GEO

Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 3T3 cell transcriptomes

Project description:Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 3T3 cell transcriptomes

| PRJNA681579 | ENA

Methylation profiling of 3T3-L1 Cells: Control vs slincRAD-shRNA8 stable transfected

Project description:Genome-wide methylation profiling of mouse 3T3-L1 Cells comparing control wildtypes with cells stable transfected with slincRAD shRNA8 (sh8). Two-condition experiment, 3T3-L1 wildtype vs. slincRAD-shRNA8 stable transfected cells before and after Adipogenesis. One replicate per array.

2016-07-01 | E-GEOD-81739 | biostudies-arrayexpress

Methylation profiling of 3T3-L1 Cells: Control vs slincRAD-shRNA8 stable transfected

Project description:Genome-wide methylation profiling of mouse 3T3-L1 Cells comparing control wildtypes with cells stable transfected with slincRAD shRNA8 (sh8).

2016-07-01 | GSE81739 | GEO

Next Generation Sequencing Facillitates Quantitative Analysis of Wild Type and snrk1a1/a2 mutant Transcriptomes

Project description:Next Generation Sequencing Facillitates Quantitative Analysis of Wild Type and snrk1a1/a2 mutant Transcriptomes

2021-12-31 | GSE183118 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and FGR Transcriptomes

Project description:Our study represents the detailed analysis of midbrain transcriptomes generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of midbrain mRNA profiles of 3-day-old wild-type (WT) and FGR mice.

2019-09-19 | GSE137660 | GEO

Quantitative Analysis of Phaeodactylum tricornutum transcriptomes

Project description:Quantitative Analysis of Phaeodactylum tricornutum transcriptomes

| PRJNA837606 | ENA

Quantitative Analysis of OxyS regulatory Transcriptomes

Project description:Quantitative Analysis of OxyS regulatory Transcriptomes

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RNA sequencing data from 3T3 cells overexpressing hPARG

Project description:3T3 malignant cell line with stable overexpression of PARG under Doxycycline induction was generated. Transcriptome analysis linked malignance reduction phenotype with changes in chemokine family and other genes' expression levels.

2022-05-11 | GSE189637 | GEO

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