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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE163479 | GEO | 2021/02/18

REPOSITORIES: GEO

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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 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 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

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-/- 4T1 mouse mammary carcinoma cell transcriptomes

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

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Ki-67 organises heterochromatin during cell proliferation

Project description:Antigen Ki-67 is a nuclear protein expressed in proliferating mammalian cells. It is widely used in cancer histopathology but its functions remain unclear. Here, we show that Ki-67 controls heterochromatin organisation. Altering Ki-67 expression levels did not significantly affect cell proliferation in vivo. Ki-67 mutant mice developed normally and cells lacking Ki-67 proliferated efficiently. Conversely, upregulation of Ki-67 expression in differentiated tissues did not inhibit cell cycle arrest. Ki-67 interactors included proteins involved in nucleolar processes and chromatin regulators. Ki-67 depletion disrupted nucleologenesis but did not inhibit pre-rRNA processing. In contrast, it altered gene expression. Ki-67 silencing also had wide-ranging effects on chromatin organisation, disrupting heterochromatin compaction and long-range genomic interactions. Trimethylation of histone H3K9 and H4K20 at heterochromatin was strongly reduced. Overexpression of human or Xenopus Ki-67 induced ectopic heterochromatin formation. Altogether, our results suggest that Ki-67 expression in proliferating cells spatially organises heterochromatin, thereby controlling gene expression.

2018-10-26 | PXD003551 | Pride

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

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Expression data for LDHA KD 4T1 cells

Project description:LDHA is key enzyme for tumor glycolysis metabolism and knocking down LDHA would change a lot of gene expression We used microarrays to detail the global gene expression in 4T1 cells with LDHA knocked down by shRNA

2017-09-16 | GSE103925 | 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

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