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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression analysis of monocytes and monocyte derived cells (MDCs) in CLL patients with differing antibody sensitivity

ABSTRACT: RNA from CD14 positive monocytes isolated from CLL patient PBMCs on day 0 and from MDCs from CLL PBMCs cultured for seven days were hybridised to an RNA microarray to identify differences between the MDCs derived from sensitive or resistant CLL patients and differences in MDCs pre and post in vitro culture. Total RNA isolated from CD14 positive monocytes from 2 sensitive and 2 resistant CLL patients and total RNA isolated from MDCs from 4 sensitive and 3 resistant CLL patients

ORGANISM(S): Homo sapiens

SUBMITTER: Nicholas Saunders

PROVIDER: E-GEOD-71409 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression analysis of monocytes and monocyte derived cells (MDCs) in CLL patients with differing antibody sensitivity

Project description:RNA from CD14 positive monocytes isolated from CLL patient PBMCs on day 0 and from MDCs from CLL PBMCs cultured for seven days were hybridised to an RNA microarray to identify differences between the MDCs derived from sensitive or resistant CLL patients and differences in MDCs pre and post in vitro culture.

2015-07-29 | GSE71409 | GEO

Transcripts differentially expressed in healthy blood mDCs compared to healthy monocytes

Project description:To directly compare the SLE monocyte transcriptional program with that of blood mDC precursors, we purified lineage HLA-DRhighCD11chigh mDCs and CD14+ monocytes from the blood of five healthy donors. Their gene expression profiles were then compared to those of blood SLE monocytes. An unsupervised clustering analysis of transcripts present in >20% of the samples classified healthy monocytes, SLE monocytes and healthy mDCs into three well defined groups. A supervised analysis was then performed to find genes: 1) differentially expressed in healthy mDCs compared to monocytes; 2) shared by healthy blood mDCs and SLE blood monocytes. To directly compare the SLE monocyte transcriptional program with that of blood mDC precursors, we purified lineage HLA-DRhighCD11chigh mDCs and CD14+ monocytes from the blood of five healthy donors. Their gene expression profiles were then compared to those of blood SLE monocytes. An unsupervised clustering analysis of transcripts present in >20% of the samples classified healthy monocytes, SLE monocytes and healthy mDCs into three well defined groups. A supervised analysis was then performed to find genes: 1) differentially expressed in healthy mDCs compared to monocytes; 2) shared by healthy blood mDCs and SLE blood monocytes.

2014-06-03 | E-GEOD-46913 | biostudies-arrayexpress

Transcripts differentially expressed in healthy blood mDCs compared to healthy monocytes

2014-06-03 | GSE46913 | GEO

Expression data from CD11c+ mDCs in HIV infection

Project description:CD11c+ Myeloid Dendritic Cells (mDCs) were isolated from the peripheral blood mononuclear cells (PBMCs) of HIV uninfected and HIV infected subjects. The expression of CD11c+ mDCs was accessed to determine how HIV infection may play a role on the expression profiles of these cells. mDCs are known to play a role in antigen presentation, and thus are pivotal in immune sensing and priming of the adaptive immune response. We wanted to see if the change in immune system function during chronic HIV infection may be due to defects in this cell subtype. We used microarray analysis to detail the global program of gene expression underlying changes in mDC function during HIV infection. PBMCs were isolated from HIV uninfected and HIV infected blood samples. CD11c+ cells were sorted from the whole PBMC population by magnetic bead sorting (anti-CD11c antibody bound to a magnetic bead inclubated with whole PBMCs). RNA was isolated from this sorted population to get the gene expression of this subtype of cells.

2012-11-07 | E-GEOD-42058 | biostudies-arrayexpress

Gene expression profiles of monocytes derived from chronic lymphocytic leukemia patients and normal controls

Project description:We collected monocytes from peripheral blood of 5 chronic lymphocytic leukemia (CLL) patients and 5 healthy donors and we performed gene expression analysis by microarray. Comparison of gene expression profiles (GEPs) between CLL-derived and normal monocytes was used to discover molecular abnormalities in this nonmalignant immune cellular population in leukemia-bearing patients. Although analysed cells were not part of the malignant clone, in unsupervised hierarchical clustering analysis, GEPs of normal monocytes were clearly distinguishable from those of monocytes obtained from CLL patients. Supervised analysis identified 65 genes significantly up-regulated and 48 genes down-regulated in CLL monocytes compared with monocytes from normal controls (FC=2, p<0.05). Modification of gene expression profile would imply impairment of phagocytosis and production of immunosuppressive mediators in CLL-derived monocytes. The alterations described in our study further contribute to characterize the complexity of factors potentially involved in acquired immune deficiency of CLL patients. Large-scale gene expression profiling (GEP) was performed on total RNA extracted from purified CD14+ monocytes (RNeasy Mini kit Plus, QIAGEN, Valencia, CA, USA) isolated from 5 individual CLL patients and 5 healthy controls by hybridization on 4X44K Whole Human Genome Microarray (Agilent Technologies, Palo alto, CA). Fluorescence data were analysed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3. Agglomerative two-dimensional clustering analysis and supervised analyses based on t-test were performed using Gene Spring GX (Agilent) software. Genes were defined as differentially expressed between groups at a significant level of p<0.05 and with a fold change cut off Â± 2 in all the pair wise comparisons.

2013-01-10 | E-GEOD-35179 | biostudies-arrayexpress

Gene predictors of response to bendamustine in CLL cells

Project description:Bendamustine is a commonly-used drug to treat CLL patients. Because drug-responses among the patients are heterogeneous, we wanted to find candidate genes to predict sensitivity to the compound We used microarrays to find genes whose expression correlates with the in vitro induced-cytotoxcity by a 24-hour incubation with bendamustine 25 µm RNA was extracted from CD19+ tumoral cells from 38 PBMCs of CLL cases

2015-05-15 | E-GEOD-68163 | biostudies-arrayexpress

RNA-seq of non-LPS treated (N), non-tolerized (NT), and tolerized (T) IFNg-primed macrophages pretreated with or without HDAC3i

Project description:In this experiment we investigated the effect of HDAC3 inhibition on the transcriptome of IFNg-primed macrophages under different tolerization conditions. Peripheral blood mononuclear cells (PBMCs) were isolated from 3 healthy donors. PBMCs were isolated from whole blood of healthy donors using Ficoll gradient (Invitrogen). Monocytes (CD14+ cells) were positively selected from PBMCs using CD14 Microbeads according to the manufacturer’s instructions (Miltenyi Biotec). Monocytes were subsequently treated with or without 500 nM HDAC3i (ITF3100) for 30 minutes prior to overnight IFNg priming (50 ng/mL). Cells were then kept without LPS (non-LPS; N), treated with 10 ng/mL LPS once (non-tolerized; NT), or treated with LPS twice (tolerized; T; second LPS concentration: 100 ng/mL).

2020-02-12 | E-MTAB-8784 | biostudies-arrayexpress

Expression data from CD11c+ mDCs in HIV infection

2012-11-07 | GSE42058 | GEO

Comparison of human plasmacytoid dendritic cells and monocyte-derived dendritic cells

Project description:Transcriptome analysis was conducted to investigate the gene expression profiles of pDCs using bulk RNA-sequencing (RNA-seq). Peripheral blood mononuclear cells (PBMCs) from healthy donors (n=3) were stained with lineage markers (CD3, CD14, CD16, CD19, and CD56), and pDCs were identified via flow cytometry (fluorescence-activated cell sorting [FACS]) based on the co-expression of IL-3R (CD123) and BDCA-2 (CD303). mDCs were identified using CD11c and sorted from the same PBMC donor as a control. After sorting, mRNA was extracted from the sorted cells, including mDCs and pDCs. The whole transcriptome profile was analyzed via RNA-seq.

2023-10-24 | E-MTAB-13390 | biostudies-arrayexpress

Gene expression profiles of TIE2 expressing Monocytes (TEMs)

Project description:To identify the gene expressing profiles of TIE2 expressing Monocytes(TEMs), we have employed the Agilent lncRNA Gene Expression 4Ã180K(Design ID:042818) microarray. Human peripheral blood mononuclear cells (PBMCs) in venous blood from healthy donors were isolated by Lymphoprep (Axis-Shield, Norway). Human monocytes in PBMCs, identified as cells that expressed CD14, were enriched by positive immunomagnetic selection using anti-CD14 MicroBeads (Miltenyi, Germany). TEMs (TIE2+CD14+) and TIE2-Monocytes (Tie2-CD14+) were then isolated by FACS-sorting (Aria II, BD Biosciences) using FITC-conjugated anti-CD14 (BD Biosciences, USA) and APC-conjugated anti-TIE2 (R&D System, USA) antibodies.Three TEMs samples together with their paried TIE2-Monocytes were detected.Expressions of sixteen genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern. The gene expressions of three independent paried TEMs and TIE2- Monocytes samples from different donors were measured.

2017-05-17 | E-GEOD-57783 | biostudies-arrayexpress

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