Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA122183 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Full title: Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication In order to identify extra cellular signals that promote B lymphocyte development we created a database with approximately 400 receptor ligand pairs and software matching gene expression data from two cell populations to obtain information about possible communication pathways. Using this database and gene expression data from NIH3T3 cells (unable to support B cell development) and OP-9 cells (strongly supportive of B cell development) and data from pro-B and pre-B cells as well as mature peripheral B-lineage cells, we were able to identify a set of potential stage and stromal cell restricted communication pathways. Functional analysis of some of these potential ways of communication allowed us to identify BMP-4 as a potent stimulator of B-cell development in vitro. Further, the analysis suggested that there existed possibilities for progenitor B cells to send signals to the stroma. The functional consequences of this were investigated by co-culture experiments revealing that the co-incubation of stromal cells with pro-B cells altered both the morphology and the gene expression pattern in the stromal cells. OP9 Stromal cells has been cultured with and without primary PreB cells drived from LSK cells in culture or PreB cell lines 230-238. OP9 cells has been isolated by FACS and microarray performed to study the effect of PreB cells on OP9's at the level of RNA expression. The results have been compared with 3T3 and MC3T3 cells.
2010-01-05 | E-GEOD-19729 | biostudies-arrayexpress
Project description:Full title: Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication In order to identify extra cellular signals that promote B lymphocyte development we created a database with approximately 400 receptor ligand pairs and software matching gene expression data from two cell populations to obtain information about possible communication pathways. Using this database and gene expression data from NIH3T3 cells (unable to support B cell development) and OP-9 cells (strongly supportive of B cell development) and data from pro-B and pre-B cells as well as mature peripheral B-lineage cells, we were able to identify a set of potential stage and stromal cell restricted communication pathways. Functional analysis of some of these potential ways of communication allowed us to identify BMP-4 as a potent stimulator of B-cell development in vitro. Further, the analysis suggested that there existed possibilities for progenitor B cells to send signals to the stroma. The functional consequences of this were investigated by co-culture experiments revealing that the co-incubation of stromal cells with pro-B cells altered both the morphology and the gene expression pattern in the stromal cells.
2010-01-05 | GSE19729 | GEO
Project description:Two-way communication between endometrial stromal cells and monocytes
| PRJNA112041 | ENA
Project description:Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street?
| PRJNA300960 | ENA
Project description:Reciprocal communication between endometrial stromal cells and macrophages
| PRJNA122051 | ENA
Project description:Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2,264 SMC1A interactions, of which 1,491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue- specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output. In contrast to previous studies, we also identified interactions between promoters and distal sites that are maintained in multiple tissues, but are poised in embryonic stem cells and resolve to tissue-specific activated or repressed chromatin states in the mouse embryo. Our results reveal the diversity of cohesin- associated interactions in the genome and highlight their role in establishing the regulatory architecture of development. Smc1a ChIA-PET, RNA-seq, chromatin state maps (H3K27ac, H3K27me3, H3K4m2), and CTCF and Smc1a binding in mouse embryonic limb bud (E11.5)
2013-05-22 | E-GEOD-42237 | biostudies-arrayexpress
Project description:Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? [Affymetrix]
| PRJNA300962 | ENA
Project description:Crosstalk between tumor and stromal cells is essential for tumor pathogenesis. Tumor and stromal interactions consist of reciprocal signaling through cytokines, growth factors, direct cell-cell interactions, and extracellular vesicles (EVs), among others. Small EVs (≤200 nm) have been considered critical messengers of cellular communication during tumor development. Here, we demonstrated that gain-of-function (GOF) p53 protein can be packaged into small EVs and transferred to stromal cells. In this study, we performed RNA sequencing to explore the gene signature alterations in small EVs after knockdown GOF p53 expression.
2020-11-18 | GSE148698 | GEO
Project description:Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? [RNA-Seq]
| PRJNA300963 | ENA
Project description:Specific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements contained within a single chromatin domain are coordinated. Recent technological advances which can detect multi-way chromatin interactions at single alleles can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. Here, we use such an approach to investigate how interactions of the α-globin enhancers are distributed between multiple promoters in a mouse model in which the α-globin domain is extended to include several additional genes. Our data show that gene promoters do not form mutually exclusive interactions with enhancers, but all interact simultaneously in a single complex. These findings suggest that promoters do not structurally compete for interactions with enhancers, but form a regulatory hub structure, which is consistent with recent models of transcriptional activation occurring in non- membrane bound nuclear compartments.
2019-10-11 | GSE130308 | GEO