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Mus musculus breed:(C57BL/6) F2-op/op

ABSTRACT: Global gene expression between stromal OP9 cells with and without expression of Pbrm1

PROVIDER: PRJNA578809 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10338915_1.fastq.gz	Fastqsanger.gz
	SRR10338915_2.fastq.gz	Fastqsanger.gz
	SRR10338916_1.fastq.gz	Fastqsanger.gz
	SRR10338916_2.fastq.gz	Fastqsanger.gz
	SRR10338917_1.fastq.gz	Fastqsanger.gz

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Vitamin C Promotes Positive Selection of Mouse T Cells

Project description:We discovered that vitamin C (ascorbic acid) is required for differentiation of mouse bone marrow-derived progenitor cells in T cell cultures based on OP9-DL1 stromal cells. This microarray dataset evaluates differential expression of genes in OP9-DL1 stromal cells as well as in lymphocytes developing in the cultures when a stabilized form of ascorbic acid (l-ascorbic acid 2-phosphate; pAsc) is added. Cultures were maintained in the absence of pAsc for 13 days, at which time 800 micromolar pAsc was added. Cells were harvested after 24 and 72 hours (24 hours only in the case of OP9-DL1 cells) and solubilized in Trizol. Two-condition experiment, differentiating T lymphoid cells with or without pAsc, 2 timepoints, OP9-DL1 cells with or without pAsc, 1 timepoint, no technical replicates

2011-08-23 | E-GEOD-31596 | biostudies-arrayexpress

Expression data from Hh signaling-deficient OP9 stromal cells

Project description:In the bone marrow B cell development occurs in initimate and essential association with stromal cells. Known effects of stromal cells on B cell development have been shown to be mediated through direct contact and by soluble factors produced by stromal cells. Our findings suggest that cell-nonautonomous Hh signaling may play an important role in B cell lymphopoiesis. We therefore interrogated OP9 stromal cells for Hh-dependent transcripts that may confer B lymphopoietic identity. We generated OP9 stromal cells deficient in Hh signaling through targeting the non-redundant, pathway-obligate GPCR Smoothened. OP9 cells were transduced with RNAi pLKO.1-Puro lentiviral particles expressing a scrambled control shRNA (NT) or shRNA targeting Smoothened (Smo-kd). RNA from stable NT and Smo-kd OP9 cells were isolated in triplicate and global changes in transcripts were analyzed using the Affymetrix Mouse Exon 1.0 ST gene chip.

2012-07-11 | E-GEOD-34421 | biostudies-arrayexpress

Mouse Bone-marrow Stromal Cell Lines Genetic Expression Comparison

Project description:OP9 stromal cells are strong inducers of mesoendodermal differentiation of human embryonic stem cells. They acquire inductive function after prolonged post-confluence culture. The experiment is designed to determine the genes specifically expressed in these highly inductive OP9 cells compared to non-confluent OP9 cultures as well as other stromal cell lines (MS5, S17).

2014-09-20 | GSE61580 | GEO

Trancriptomic profiling of HCT116 colon cancer cells with or without PBRM1 knock-down by RNAi

Project description:To investigate the influence of PBRM1 on gene expression, we performed RNA-seq in HCT116 colon cancer cells with or without PBRM1 knock-down by RNAi (both shRNA and siRNA approaches were used), and identified differentially expressed genes in PBRM1 knock-down cells compared to control cells, which shows implications for PBRM1's biological function in colon cancer.

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Interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication

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.

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Gene expression profile at single cell level of crude umbilical cord blood (UCB) and OP9 pre-conditioned UCB.

Project description:Umbilical cord blood (UCB) transplantation shows pro-angiogenic effect and contributes to symptom amelioration in animal models of cerebral infarction. OP9 is a stromal cell line used as feeder cells to promote hematoendothelial differentiation of embryonic stem cells. We co-cultured UCB 24hr with OP9 (i.e. OP9 preconditioning) and investigated its change in angiogenic properties and underlying mechanisms. Single cell RNA sequencing showed prominent phenotypic shift toward M2 in monocytic fraction of OP9 pre-conditioned UCB.

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Project description:Hemogenic endothelium (HE) is the source of HSCs in the developing embryo. In this study we have identified the hemogenic endothelial progenitors and their precursors originating from differentiated H1 cells on OP9 stromal cells. RNA-seq of hemogenic endothelial progenitors and their precursors originating from differentiated H1 cells on OP9 stromal cells.

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Lhx2-regulated genes in hematopoietic stem cell (HSC)-like cells differentiated from mouse embryonic stem (ES) cells

Project description:We previously demonstrated that hematopoietic stem cell (HSC)-like cells are robustly expanded from mouse embryonic stem (ES) cells by enforced expression of Lhx2, a LIM-homeobox domain (LIM-HD) transcription factor. Here we established an ES cell line which conditionally expressed Lhx2 by Tet-On system. The ES cells were differentiated into HSC-like cells by Lhx2 expression. Lhx2-regulated genes were identified by comparing the HSC-like cells with those cultured in the absence of Lhx2 expression. Mouse ES with inducible Lhx2 were differentiated on OP9 stromal cells into hematopoietic lineage. On day 5 of the differentiation induction,Lhx2 expression was started by the addition of doxycycline (dox) and the cells were cultured on OP9 stromal cells in the presence of IL-6 and SCF. On day 20, HSC-like cells were harvested and re-seeded onto OP9 stromal cells in the absence of Lhx2 expression by dox-removal for 3 days. these cells were compared with the original HSC-like cells.

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Mus musculus

Project description:Expression data from Hh signaling-deficient OP9 stromal cells

| PRJNA149549 | ENA