Comparative genomic hybridization by array of 12 human bone marrow samples from Faconi anemia bone marrow to investigate effects of Eurofancolen
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Jean Soulier
PROVIDER: E-MTAB-8139 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Arrays-CGH and/or SNP-array data from n=57 Fanconi anemia BM and n=36 paired fibroblasts
2011-07-28 | E-MTAB-529 | biostudies-arrayexpress
Project description:We hypothesize that under homeostatic as well as inflammatory conditions circulating monocytes and/or their bone marrow-derived progenitors might contribute to the replenishment of CD103+ and CD103- DC in lymphoid and non-lymphoid compartments. To that end, bone marrow cells from CX3CR1+/gfp C57BL/6 mice were sorted as follows: lineage negative (CD3, CD19, NK1.1, Ter119, Ly6G and CD11c) CX3CR1+c-kit+. Sorted cells were further cultured in vitro under the continuous presence of GM-CSF. lin-CX3CR1+c-kit+ bone marrow cells gave rise to CD103+ and CD103- DC in vitro. To test whether CD103 might be a suitable marker that allows the differentiation of functionally distinct DC subsets generated in vitro, CD11c+CD103+ and CD11c+CD103- DC were sorted from day 5 cultures of lin-CX3CR1+c-kit+ cells and analyzed by whole mouse genome microarrays from Agilent technologies. Compared to CD103+ DC, CD103- DC displayed a strong up-regulation of transcripts for genes involved in innate immunity, whereas those involved in costimulation were down-modulated. Our data suggest distinct functional activity of these two DC subsets. Keywords: Transcriptional profiling-Cell type comparison We compared the transcriptional profile of CD11c+CD103+ and CD11c+CD103- dendritic cells by use of Agilent Whole Mouse Genome Microarrays. Two sets of samples were generated independently as real biological replicates. The microarray analysis was performed as a dual-color experiment, including a dye-swap.
2008-12-17 | E-GEOD-10882 | biostudies-arrayexpress
Project description:RATIONALE: Radiation therapy uses high-energy x-rays to damage cancer cells. Drugs used in chemotherapy use different ways to stop cancer cells from dividing so they stop growing or die. Combining chemotherapy with bone marrow transplantation may allow the doctor to give higher doses of chemotherapy drugs and kill more tumor cells.
PURPOSE: Phase II trial to study the effectiveness of bone marrow transplantation in treating patients who have hematologic cancer.
| 2004880 | ecrin-mdr-crc
Project description:Dental caries is closely associated with the virulence of Streptococcus mutans (S. mutans). The stress adaptation of S. mutans in the fluctuating oral environment is critical to the virulence expression of this bacterium. Here we used whole-genome microarrays to profile the dynamic transcriptomic responses of S. mutans during physiological heat stress. We also evaluated the phenotypic changes, including initial biofilm formation, acid production and ATP turnover of S. mutans during heat stress. We found that S. mutans responded to heat stress in a distinct pattern, which featured a differential transcription of 885 genes in total and 114 “core” transcripts throughout the six post-exposure time points investigated (5 min, 10 min, 15 min, 30 min, 45 min and 60 min). Further gene ontology analysis showed that transcriptional changes of genes involved in transcriptional regulation and cellular homeostasis were critical for heat stress responses of S. mutans. In addition to those highly conserved heat-shock proteins, we observed differential expression of multiple transcriptional regulators. The expression of genes involved in sugar transport, soluble glucans biosynthesis (gtfC) and binding (gbpC) were upregulated, whereas genes involved in ABC transporters, insoluble glucans biosynthesis (gtfB) and binding (gbpB), which are critical for biofilm skeleton, were either down-regulated or unchanged. These results together with enhanced glycolytic activity, attenuated sucrose-dependent initial attachment and impaired biofilm architecture indicate metabolic adaptations by this bacterium to compensate the extra energy demand for a better fitness under adverse conditions. We used time series microarrays to detect the dynamic changes of S. mutans under heat stress. Mid-logarithmic phase cell cultures of S. mutans (OD600nm = 0.5) were incubated at 42℃ for 5 min, 10 min, 15 min, 30 min, 45 min and 60 min, which were compared with the S. mutans cultured at 37℃. We applied three biological replicates at each time point.
2014-10-01 | E-GEOD-59302 | biostudies-arrayexpress
Project description:Human bone marrow mesenchymal stromal cells (BM-MSC) could be committed toward a functional lymphoid-like stroma by a combination of TNFalpha (TNF) and Lymphotoxin alpha1/beta2 (LT) (Amé-Thomas et al Blood 2007). Bone marrow and lymph node stromal cells support FL malignant cell recruitment and growth in particular after comittment to a lymphoid-like differentiation in vitro. In addition, more than 70% of FL patients exhibit a bone marrow involvment at diagnosis. We delineate using Affymetrix U133+2.0 microarrays the gene expression profile of BM-MSC obtained from FL patients (FL-MSC) and age-matched healthy donors (HD-MSC) in order to identify a specific FL-MSC signature. In addition, we used Affymetrix microarrays to define the gene expression signature of lymphoid-like stromal cells obtained from HD-MSC by treatment with TNF/LT in vitro. This TNF/LT signature was then used to interpret the gene expression profile of FL-MSC. GEP was performed on 10 BM-MSC from FL patients and 6 from healthy donors, treated or not with TNF(10 ng/mL)/LT(100ng/mL)
2012-01-26 | E-GEOD-35331 | biostudies-arrayexpress
Project description:Nucleotide signaling pathways are found in all kingdoms of life and are utilized to coordinate a rapid response to changes in the environment. One more recently discovered signaling nucleotide is the secondary messenger cyclic diadenosine monophosphate (c-di-AMP), which is widely distributed among bacteria and is also found in several archaea. This cyclic nucleotide has been shown to involve in several important cellular processes, including maintenance of DNA integrity, cell wall metabolism, stress tolerance, transcription regulation and virulence. However, the mechanisms by which c-di-AMP modulates these physiological changes have remained largely unknown.In the present study, we identified and characterized a c-di-AMP synthase (CdaA) in S. mutans UA159. Furthermore, we investigated the role of CdaA in S. mutans cell physiology and global gene expression by utilizing cdaA gene in-frame deletion mutant. Our findings suggest that CdaA is an important global modulator of optimal growth and environmental adaption in this pathogen. Streptococcus mutans UA159 whole-genome arrays (8 x 15 K) were obtained from Agilent and included 1998 probes for S. mutans transcripts. For microarray analysis, S. mutans UA159 and S. mutans ?cdaA cells were routinely grown at 37°C anaerobically (90% N2, 5% CO2, 5% H2) in brain heart infusion broth (BHI; Difco, Sparks, MD, USA) to an optical density at 600 nm (OD600) of 0.5. Four RNA samples isolated from four independent cultures of UA159 and cdaA mutant strains were hybridized to the arrays and analyzed.
2015-04-06 | E-GEOD-65511 | biostudies-arrayexpress
Project description:This phase II trial studies how well giving fludarabine phosphate, cyclophosphamide, tacrolimus, mycophenolate mofetil and total-body irradiation together with a donor bone marrow transplant works in treating patients with high-risk hematologic cancer. Giving low doses of chemotherapy, such as fludarabine phosphate and cyclophosphamide, and total-body irradiation before a donor bone marrow transplant helps stop the growth of cancer cells by stopping them from dividing or killing them. Giving cyclophosphamide after transplant may also stop the patient’s immune system from rejecting the donor’s bone marrow stem cells. The donated stem cells may replace the patient’s immune system cells and help destroy any remaining cancer cells (graft-versus-tumor effect). Sometimes the transplanted cells from a donor can also make an immune response against the body’s normal cells. Giving tacrolimus and mycophenolate mofetil after the transplant may stop this from happening
| 2008483 | ecrin-mdr-crc
Project description:The Mef2 family transcriptional regulator Mef2c is highly expressed in maturing bone marrow and peripheral mature B cells. To evaluate the role of this transcription factor in B cell development, we generated a B cell specific conditional deletion of Mef2c using the Mb-1-Cre transgene that is expressed during the early stages of immunoglobulin rearrangement. Young mice possessing this defect demonstrated a significant impairment in B cell numbers in bone marrow and spleen. This phenotype was evident in all B cell subsets; however, as the animals mature, the deficit in the peripheral mature B cell compartments was overcome. The absence of Mef2c in mature B cells led to unique CD23+ and CD23- subsets that were evident in Mef2c KO primary samples as well as cultured, differentiated B cells but not in WT cell populations. Genome wide expression analysis of immature and mature B cells lacking Mef2c indicated altered expression for a number of key regulatory proteins for B cell function including Ciita, CD23, Cr1/Cr2, and Tnfsf4. Chromatin immunoprecipitation analysis confirmed Mef2c binding to the promoters of these genes indicating a direct link between the presence (or absence) of Mef2c and altered transcriptional control in mature B cells. Four samples are submitted.
2012-05-31 | E-GEOD-34210 | biostudies-arrayexpress