B cells and peritoneal macrophages RNA-seq
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ABSTRACT:
PROVIDER: PRJNA925426 | ENA |
REPOSITORIES: ENA
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Project description:RNA seq of wild-type C57B6/L mouse peritoneal macrophages with infection of SeV (MOI=1) for 12 hours.
2024-05-01 | GSE230756 | GEO
Project description:We found that CD11b-expressing B cells were increased in the BM of LPS-treatmed mice. To examine the differences in gene expression, we isolated CD11b-negative and CD11b-positive B cells were isolated and compared the gene expression profiles with peritoneal macrophages obtained from naive mice by RNA-sequence.
2023-01-24 | GSE222966 | GEO
Project description:Primary peritoneal macrophages were obtained from the peritoneal exudates of mice that were pretreated with 3% thioglycolate (LA4590, Solarbio) i.p. for 5 days. The peritoneal exudate cells were collected by cold PBS and adjusted to 1 × 10^6 cells/ml in DMEM cultured at 37C and 5% CO2 in a cell incubator. At 2 hours later, after using PBS to wash out the supernatant cells, the remaining adherent cells contained more than 90% F4+/80+ macrophages by flow cytometry analysis. Peritoneal macrophages were treated with 100ng/ml of recombinant murine BMP9 or Vehicle for 6h to activate macrophages.Then, send to RNA seq,
2024-02-18 | GSE230030 | GEO
Project description:We report here the deep sequencing of the mRNA from peritoneal exudate cells (macrophages) purified from wildtype or Ptpn1 (PTP1B) knockout mice, either treated or untreated with IL-10. In periotenal macrophages IL-10 activates the transcription factor STAT3 to execute and anti-inflammatory gene expression programme. The tyrosine phosphatase PTPN1 targets STAT3 for dephosphorylation and leads to the deactivation of STAT3. In this study we examined the role of PTP1B in controlling the normal homeostatic level phosphorylation of STAT3 by comparing the IL-10/STAT3-mediated anti-inflammatory gene expression programme. We find that loss of PTP1B leads to an up-regulation of the activity of STAT3, both at the level of phosphorylation and also in enhanced expression of anti-inflammatory gene products. RNA-seq of wildtype and Ptpn1 (PTP1B) knockout mouse peritoneal macrophages, treated or untreated with IL-10
2014-05-12 | E-GEOD-49449 | biostudies-arrayexpress
Project description:The interaction of macrophages with apoptotic cells is required for efficient resolution of inflammation. While apoptotic cell removal prevents inflammation due to secondary necrosis, it also alters the macrophage phenotype to hinder further inflammatory reactions. The interaction between apoptotic cells and macrophages is often studied by chemical or biological induction of apoptosis, which may introduce artifacts by affecting the macrophages as well and/or triggering unrelated signaling pathways. Here, we set up a pure cell death system in which NIH 3T3 cells expressing dimerizable Caspase-8 were co-cultured with peritoneal macrophages in a transwell system. Phenotype changes in macrophages induced by apoptotic cells were evaluated by RNA sequencing, which revealed an unexpectedly dominant impact on macrophage proliferation. This was confirmed in functional assays with primary peritoneal macrophages and IC-21 macrophages. Moreover, inhibition of apoptosis during Zymosan-induced peritonitis in mice decreased mRNA levels of cell cycle mediators in peritoneal macrophages. Proliferation of macrophages in response to apoptotic cells may be important to increase macrophage numbers to allow efficient clearance and resolution of inflammation.
2021-03-18 | GSE164709 | GEO
Project description:Apoptotic cells induce proliferation of peritoneal macrophages
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Project description:Local factors produced in the tissue microenvironment play essential roles in promoting the ontogeny and phenotype of tissue resident macrophages (TRM). In the peritoneal cavity, large peritoneal macrophages (LPM) are the dominant TRMs that functionally mediate type 2 immunity, facilitate tissue repair of the mesothelium, and protect against peritoneal fibrosis. It is established that retinoic acid derived from the omentum induces transcription factor Gata6 expression in LPMs, which in turn regulates gene expression of factors that define peritoneal macrophages. It is still unclear whether retinoic acid is the sole local factor that regulates Gata6 expression in LPMs. Mesothelial cells line the entire peritoneal cavity and produce a protective, non-adhesive barrier against injury, at least in part by recruiting immune cells with secreted cytokines, such as M-CSF. We hypothesized that secreted factors from peritoneal mesothelial cells are also responsible for regulating LPM development including both ontogeny and function. Due to their immediate proximity to the peritoneal cavity, we propose that mesothelial cells can produce and secrete proteins into the peritoneum to maintain Gata6 expression by LPMs. To identify secreted factors that are highly and specifically expressed in mesothelial cells, we harvested primary mesothelial cells from 10-week-old C57BL/6 mice using FACS selection (CD45- PDPN+ GPM6a+). Total RNA was isolated from these cells and subjected to RNA-seq analysis after depletion of ribosomal RNA.
2020-08-01 | GSE129391 | GEO
Project description:Purpose: Previous work has demonstrated that miR-33 is an important regulator of lipid metabolism and atherogenesis. By performing bone marrow transplant experiments into LDLR-/- mice, our work demonstrates that the effects of miR-33 in macrophages play a major role in its ability to reduced atherosclerotic plaque burdon. To have performed extensive additional characterization of the effects of miR-33 deficiency in macrophages icluding RNA-seq analysis of peritoneal macrophages from wildtype, miR-33-/-, LDLR-/-, and miR33-/-/LDLR-/- animals. Methods: Thioglycolate elicited peritoneal macrophages from WT and miR-33-/- mice were harvested by peritoneal lavage. Cells were then plated for 2hr, then washed to remove non-adherant cells. Macrophages were then scraped, pelleted and frozen at -80◦C. Total RNA from WT and miR-33-/- thioglycollate-elicited peritoneal macrophages was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). The purity and integrity of total RNA sample was verified using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries from WT BMDMs were performed TrueSeq Small RNA Library preparation (Illumina) and were sequenced for 45 cycles on Illumina HiSeq 2000 platformm (1 x 75bp read length). The reads obtained from the sequencer are trimmed for quality using in-house developed scripts. The trimmed reads are aligned to the reference genome using TopHat2. The transcript abundances and differences calculated using cuffdiff. The results were plotted using R and cummeRbund using in-house developed scripts. Results: Our RNA-seq analysis has allowed us to identify genes and pathways that are altered in miR-33 deficient peritoneal macrophages under hyperlipidemic conditions (LDLR-/- vs. miR33-/-/LDLR-/-). Further analysis of gene expression changes that occur between wildtype and LDLR-/- animals has allowed us to identify which of these changes are likely due to differences in lipid loading and which are independent of these effects.
2018-02-13 | GSE103133 | GEO
Project description:B1 cells account for the majority of B cell population in the peritoneal cavity, and are essential for the innate immune responses and maintaining the homeostasis. The origin of the B1 cells and how to form the B1 cells pool in the postnatal life remain unknown. And the heterogeneity of B1 cells can largely affect the functions of B1 cells. Until now, nobody has performed the single cell RNA-seq of peritoneal B cells. In order to reveal the characteristics of peritoneal B cells, we have performed the scRNA-seq and scBCR-seq of the peritoneal B cells of mouse from different stages.
2022-05-21 | E-MTAB-10081 | biostudies-arrayexpress
Project description:Purpose: Characterize the gene expression profile of wild-type and Zeb1 (+/-) peritoneal mouse macrophages through RNA sequencing Methods: RNA sequencing of RNA from peritoneal macrophages isolated by peritoneal lavage and FACS sorting (F4/80+ CD11b+) from wild-type and Zeb1 (+/-) mice (2 mice pooled for each sample/set) Results: Wild-type and Zeb1 (+/-) peritoneal mouse macrophages display differential gene expression. Zeb1 (+/-) peritoneal macrophages express lower levels of SPM (F4/80low)-associated genes Conclusions: Wild-type and Zeb1 (+/-) peritoneal mouse macrophages display differential gene expression. Zeb1 (+/-) peritoneal macrophages express lower levels of SPM (F4/80low)-associated genes
2019-05-24 | GSE103830 | GEO