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Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 4T1 mouse mammary carcinoma cell transcriptomes

ABSTRACT: Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 4T1 mouse mammary carcinoma cell transcriptomes

PROVIDER: PRJNA681594 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 4T1 mouse mammary carcinoma cell transcriptomes

Project description:Purpose: The goals of this study were to compare gene expression profiles of mouse 4T1 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: Ki-67 knockout causes genome-scale transcriptome alterations

2021-02-18 | GSE162358 | GEO

Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 4T1 mouse mammary carcinoma cell histone modification

Project description:Ki-67 chromatin associated proteins that has been shown to broadly affect the transcription profiles of cells when knocked-out. To understand if those transcriptome changes are regulated by histone modifications we performed ChIP-seq analysis for three of the most recognized histone marks (H3K27me3, H3K4me3 and H3K27ac) as the regulators of gene expression, in wild-type (WT) and Ki-67 knockout (Mki67−/−) mouse 4T1 cells.

2021-02-18 | GSE163479 | GEO

Next Generation Sequencing Quantitative Analysis of the transcriptomes of Wild Type and Mki67-/- 4T1 tumors in mice

Project description:Purpose: The goals of this study were to compare gene expression profiles of mouse xenografted 4T1 tumors with intact or disrupted Mki67 gene. Methods: mRNA profiles of wild-type (WT) and Ki-67 knockout (Mki67−/−) mouse xenografted 4T1 tumors, in triplicate, were generated by deep sequencing using Illumina Hiseq2500 in paired-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 Conclusions: Ki-67 knockout causes genome-scale transcriptome alterations

2021-02-18 | GSE162885 | GEO

Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 4T1 mouse mammary carcinoma cell histone modification

Project description:Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 4T1 mouse mammary carcinoma cell histone modification

| PRJNA686362 | ENA

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 the transcriptomes of Wild Type and Mki67-/- 4T1 tumors in mice

Project description:Next Generation Sequencing Quantitative Analysis of the transcriptomes of Wild Type and Mki67-/- 4T1 tumors in mice

| PRJNA683635 | ENA

Single cell RNA-seq of 4T1-T vasculogenic mimicry-competent mammary tumors

Project description:We have previously described a sub-clones of the 4T1 mammary carcinoma cell line that are proficient for vasculogenic mimciry (VM), namely 4T1-E and 4T1-T. In vitro assays suggest that not all cells within these lines a VM-competent. To explore subsets of cells within tumors derived from these cells that may display VM properties we utilized single cell RNA-Seq of 4T1-T mammary fat-pad tumors.

2023-07-26 | GSE230642 | GEO

Next Generation Sequencing Quantitative Analysis of the transcriptomes of Wild Type and Mki67-/- MDA-mb231 (human breast adenocarcinoma) cell line

Project description:Purpose: The goals of this study were to compare gene expression profiles of MDA-mb231 cell lines with intact or disrupted Mki67 gene. Methods: mRNA profiles of wild-type (WT) and three Ki-67 knockout (Mki67−/−) clones in the MDA-mb231 cell line, were generated by deep sequencing using DNBSEQ-G50 in paired-end read mode, 100bp. 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 (GRCh38) and identified differentially expressed genes. This revealed widespread changes in gene expression Conclusions: Ki-67 knockout causes genome-scale transcriptome alterations

2021-02-18 | GSE162879 | GEO

Transcript profiling of mouse 4T1 tumors grown in preirradiated vs. nonirradiated mammary tissue

Project description:The present study was designed to identify genes induced by irradiation in the 4T1 breast cancer model mimicking aggressive local relapse after radiotherapy. For this purpose, we obtained the transcriptomes of 4T1 tumors grown in either preirradiated (IRR+4T1) or non-irradiated (4T1) mammary tissue.

2017-08-31 | GSE64193 | GEO

Expression analysis of the effect of overexpression of Cebpb shRNA in mouse 4T1 mammary tumor cells

Project description:Investigation of whole genome gene expression level changes in mouse 4T1 mammary tumors expressing Cebpb shRNA, compared to 4T1 tumors expressing control shRNA. Analysis of mouse 4T1 mammary tumors expressing Cebpb shRNA compared to control shRNA are further described in Johansson & Berg et al 2012.

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