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Next Generation Sequencing Facilitates Quantitative Analysis of Epithelial cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

ABSTRACT: We had one goal to perform this study: transcriptome of Epithelial cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

ORGANISM(S): Mus musculus

PROVIDER: GSE286383 | GEO | 2025/07/31

REPOSITORIES: GEO

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Next Generation Sequencing Facilitates Quantitative Analysis of Col1a2+ stromal cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

Project description:We had one goal to perform this study: transcriptome of Col1a2+ stromal cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

2025-07-31 | GSE286027 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Col1a2+ stromal cells sorted from Col1a2-creERT Bmpr1a and ctrl mice

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Next Generation Sequencing Facilitates Quantitative Analysis of Epithelial cells sorted from Col1a2-creERT Bmpr1a and ctrl mice

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Epithelial cells sorted from Col1a2-creERT Bmpr1a and ctrl mice

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Next Generation Sequencing Facilitates Quantitative Analysis of distal part of the auricle from three Prrx1-CreERT;Bmpr1af/f and age- and gender-matched control mice.

Project description:We had one goal to perform this study: Analysis of distal part of the auricle from three Prrx1-CreERT;Bmpr1af/f and age- and gender-matched control mice.

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Hormone-responsive Bmpr1a maintains myoepithelial integrity during pregnancy

Project description:Myoepithelial and luminal cells synergistically expand in the mammary gland during pregnancy, and this process is precisely governed by hormone-related signaling pathways. The BMP signaling pathway is now known to play crucial roles in all organ systems. However, the functions of BMP signaling in the mammary gland remain unclear. Here, we found that Bmpr1a is upregulated by hormone-induced Sp1 at pregnancy. Using a doxycycline (Dox)-inducible Bmpr1a conditional knockout mouse model, we demonstrated that loss of Bmpr1a results in compromised myoepithelial integrity, reduced mammary stem cells and precocious alveolar differentiation during pregnancy. Mechanistically, Bmpr1a regulates the expression of p63 and Slug, two key regulators of myoepithelial maintenance, through pSmad1/5-Smad4 complexes, and consequently activate P-cadherin during pregnancy. Collectively, these findings identify a novel role of BMP signaling in maintaining the identity of myoepithelial cells and suppressing precocious alveolar formation.

2021-03-05 | GSE164550 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in Ctrl-Cas9 and TRIB3-Cas9 lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-Cas9 and TRIB3-Cas9 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' 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.

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Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in Ctrl-siRNA and c-Myc-siRNA lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-siRNA and c-Myc-siRNA cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ctrl-siRNA and c-Myc-siRNA cells' 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.

2020-10-02 | GSE126739 | GEO

Next-generation RNA Sequencing and Transcriptome Comparison of Mouse Wild Type and Mesenchymal Bmpr1a conditional knockout lungs of E15.5

Project description:Lung mesenchymal knockout of Bmpr1a will lead to lung malformation, including impaired lung branching and cystic lesion. In order to understand the underlying mechanisms, total RNA of wild type and mesenchymal Bmpr1a knockout lungs were isolated and sequenced using the next-generation RNA sequencing technique.

2024-04-01 | GSE97946 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of WT and GSH or Ctrl and Cas9 mouse breast cancer cells Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in WT and WT+GSH or Ctrl-Cas9 and Scarb2-Cas9 mouse breast cancer cells by using NGS-derived transcriptome profiling (RNA-seq). Methods: 4T1 cells treated with or without GSH (500 µM) and 4T1 stably expressing Ctrl-Cas9 or Scarb2-Cas9 were collected. These cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of WT and WT+GSH or Ctrl-Cas9 and Scarb2-Cas9 mouse breast cancer cells' 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.

2024-10-09 | GSE252087 | GEO

Profile of Bmpr1a-/- embryonic stem cells in ESC media and N2B27

Project description:A fundamental question in developmental biology is whether there are mechanisms to detect stem cells with mutations that although do not adversely affect their viability, would compromise their ability to contribute to further development. Here we show that cell competition is a novel mechanism regulating the fitness of embryonic stem cells (ESCs). We find that ESCs displaying defective BMP signalling, defective autophagy or are tetraploid are eliminated at the onset of differentiation by wild-type cells. This elimination occurs in an apoptotic dependent manner and is mediated by secreted factors. Furthermore, during this process we find that establishment of differential cMyc levels is critical and that cMyc over-expression is sufficient to induce competitive behaviour in ESCs. Cell competition is therefore a process that allows recognition and elimination of defective cells during the early stages of development and is likely to play important roles in tissue homeostasis and stem cell maintenance. We used microarrays to compare the gene expression profiles of Bmpr1a-/- and control embryonic stem cells (ESCs) in the ESC state and after differentiation in N2B27 Microarray profiles of control and Bmpr1a-/- mouse embryonic stem cells in embryonic stem cell culture media and in N2B27

2013-06-20 | E-GEOD-48092 | biostudies-arrayexpress

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