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Effect of LL-2 conditional medium on bone marrow-derived macrophages

ABSTRACT: To investigate the effect on LL-2 conditional medium on bone marrow-derived macrophages, equal volum of LL-2 conditional medium and fresh RPMI 1640 was used to culture bone marrow-derived macrophages for 24 hours. The cells were then lysed for RNA-seq.

ORGANISM(S): Mus musculus

PROVIDER: GSE210767 | GEO | 2023/08/06

REPOSITORIES: GEO

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Genome-wide sequencing of cultured MDSCs obtained from bone marrow of lnc57Rik ko , lncGM1082 ko and WT mice.

Project description:To fully elucidate the effects of long non-coding RNA 5730403I07Rik (lnc57Rik) and lncGM1082 on myeloid-derived suppressor cell (MDSCs), we generated lnc57Rik knockout (KO) and lncGM1082 ko mice. Then bone marrow cells were obtained from the femurs of C57BL/6, lnc57Rik KO, or lncGM1082 ko mice and cultured in RPMI-1640 medium supplemented with GM-CSF plus IL6 for 4 days. We further performed a high-throughput sequencing analysis in cultured MDSCs obtained from bone marrow of lnc57Rik ko, lncGM1082 ko and wild type (WT) mice.

2022-03-03 | GSE197566 | GEO

Expression Data from BALB/c and Stat6-deficient bone marrow derived macrophages (BMDM)

Project description:We used microarrays to find Stat6 dependent genes in control and IL-4 exposed bone marrow derived macrophages. Alternatively activated macrophages (AAM) accumulate in tissues during Th2-associated immune responses like helminth infections and allergic disorders. These cells possess potent inhibitory activity against T cells. The differentiation of AAM depends on IL-4/IL-13-mediated activation of the transcription factor Stat6. Stat6 is also required in AAM to induce several genes, such as YM1, FIZZ1 and Arginase1. Macrophages were differentiated from bone marrow cells in supplemented RPMI 1640 for 7 days in the presence of 10% supernatant from the M-CSF producing fibroblast cell line L929. After removal of nonadherent cells, macrophages were detached using 5mM EDTA treatment, washed, counted, and replated at a density of 10x6 cells/mL. Macrophages were cultured for 24 hours in medium (control) or in the presence of IL-4 (10mg/mL). F4/80 positive macrophages were sorted with a purity of 99% and RNA was isolated (Trizol/Chloroform) according to the manufacturer's instructions. RNA was labeled (biotin), fragmented, and hybridized to the arrays according to the manufacturer's recommendations.

2010-07-19 | E-GEOD-20030 | biostudies-arrayexpress

786-O ubiquitiome - Loss of BAP1 Results in Growth Inhibition and Enhances Mesenchymal-Epithelial Transition in Kidney Tumor Cells

Project description:786-O WT and BAP1-KO cells were cultured in heavy (13C6-L-arginine, 13C6-L-lysine, Cambridge Isotope Lab) and light (unlabeled L-arginine and L-lysine) SILAC RPMI-1640 medium (Thermo Fisher Scienific), respectively. After more than 10 passages, cells were lysed with 8 M urea and 5 mg protein from each group were mix. The ubiquitinated peptide enrichment was performed using PTMScan® (Cell Signaling Technology, #5562) following the manufacturer’s instructions.

2019-04-18 | PXD013127 | Pride

Comparative analysis of gene expression in response to LL-37 treatment

Project description:To identify the potential LL-37-responsed genes, we treated cells with or without LL-37 and their correspondent transcriptional profiles were compared. Total 104 significant genes were identified. Among them, 70 genes are upregulated in repsonse to LL-37 while 34 genes are downregulated in comparison with the control cells. LL-37 responsed gene was measured after 3 h growth in YPD followed by 30 min of incubation in the presence of 5 ug/ml LL-37 in RPMI. Two batches of five independent experiments were performed.

2016-03-11 | E-GEOD-45177 | biostudies-arrayexpress

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Next Generation Sequencing Facilitates Quantitative Analysis of Bone Marrow Derived Mast Cell Transcriptomes

Project description:Purpose:The purpose of this study is to detect activated or silenced genes during Tet2-deficient bone marrow derived mast cell (BMMC) and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods:Mouse BMMCs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse IL-3 and SCF. BMMCs were stained to confirm the surface expression of FcɛRI and c-Kit. Cells with purity >97.5% were used for subsequent experiments. BMMCs RNA profiles were generated by deep sequencing,using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between Tet2-deficient BMMC and the control cells.

2018-01-25 | GSE100560 | GEO

RNA-seq analysis of the effect of BSA and NaOH added to standard culturing medium on THP-1 macrophages

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2019-05-17 | E-MTAB-6439 | biostudies-arrayexpress

PU.1 interactome mouse bone marrow derived dendritic cells

Project description:Mouse bone marrow derived dendritic cells were generated by culturing bone marrow cells at a density of 0.5x10E6 cells/ml in RPMI-1640 supplemented with 5% FCS, 1% Pen/Strep, 5microM 2-mercaptoethanol, 20ng/ml GM-CSF. At day 7 dendritic cells were stimulated or not with 500 ng/ml LPS, and collected at day 10. 2x10E8 cells were used to prepare whole cell extracts and to perform PU.1 immunoprecipitaion with PU.1 antibody (T-21 Santa Cruz). IgG was used as control.

2018-11-30 | MSV000083176 | MassIVE

Differential impact of high-salt levels in vitro and in vivo on macrophage core functions

Project description:We analyzed the gene expression differences in RNA-seq data of murine bone-marrow derived macrophages (BMDM) in response to treatment with NaCl. RNA of 3 samples differentiated in vitro for 8 days using M-CSF and treated with RPMI medium or RPMI medium containing additional 62mM NaCl, respectively, was isolated with trizol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol and 100 ng of RNA was converted into cDNA libraries using the TruSeq RNA library preparation kit v2 for 75 bp single read sequencing performed on a HiSeq1500. We aligned the reads using STAR and performed downstream expression analysis in R using DESeq2.

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Distinct 5-methylcytosine profiles in poly(A)RNA from mouse bone marrow derived mast cells

Project description:Purpose: To transcriptome widely reveal 5-mC regulation by Tet2, we performed bisulfite-sequencing of mRNAs from Tet2-deficient BMMCs and the control cells.Methods: Mouse BMMCs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse IL-3 and SCF. BMMCs were stained to confirm the surface expression of FcɛRI and c-Kit. Cells with purity >97.5% were used for RNA isolation. Results: We carried out an unbiased global analysis of m5C in poly(A)RNA of mouse bone marrow derived mast cells (BMMCs).We show that there were indeed much more mCs in Tet2-deficient group compared with the control, more than half of which located in genic region. Furthermore, we observed that although much less mCs distributed in the three elements of exon regions, more mCs located in 3`-UTR for Tet2-deficient group compared with the control.

2018-01-25 | GSE100719 | GEO

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