Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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CDDP treatment of U2OS cells with NCOR and SMRT knock-down

ABSTRACT: We detected an interaction between checkpoint kinase Chk2 and some members of the NCOR/SMRT co-repressor complex. In order to study the role of gene repression in the checkpoint response to DNA damage, we performed RNA profiling in NCOR or SMRT knockdown cells after treztment with cisplatin. U2OS cells were transfected with siRNAs for NCOR or SMRT, grown for 2 days in complete medium, and then treated with 100 microM cisplatin (CDDP) for 6h. Biological duplicates were used for RNa profiling

ORGANISM(S): Homo sapiens

SUBMITTER: Claudio Scafoglio

PROVIDER: E-GEOD-34226 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the expression of the E-protein antagonist Id2. Hematopoietic progenitors that express Id2 are multipotent and readily differentiate upon withdrawal of Id2 expression into committed B lineage cells, thus indicating a causative role for E2A in promoting the B cell fate. Genome-wide analyses revealed that a substantial fraction of lymphoid and myeloid enhancers are pre-marked by H3K4me1 in multipotent progenitors. However, H3K4me1 levels at a subset of enhancers are elevated during developmental progression, resulting in evolving enhancer repertoires that we propose orchestrate the myeloid and B cell fates. ChIP-Seq and gene expression profiling were performed in an inducible hematopoietic pluripotent cell line that can be differentiated into multiple lymphoid lineages. This submission contains gene expression profiling data. To compare the expression signatures from differentiated B- and myeloid-cells derived from hematopoietic progenitors that express Id2, Id2-HPCs were differentiated into either CD19+ B cells or CD11b+ myeloid cells. The gene expression profiles of differentiating B cells at 6-, 12-, 24-, 48-, 72-, 120-, and 240-hour time points were also investigated. RNA was isolated from the cultures and analyzed by microarray gene expression analysis. Id2-HPCs were cultured in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL7, Flt3-ligand, and SCF cytokines on S17 feeder cells in a humidified incubator at 37 degrees C with 5% CO2. Id2-HPC expanded cells were depleted of small (<1-5%) numbers of CD19-, CD25- and CD11b-positive cells by auto-MACS. For myeloid differentiation, cells were cultured for up to 6 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL3, Flt3L, GMCSF and MCSF cytokines. To promote B-cell differentiation, cells were cultured for up to 10 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL-7 and SCF cytokines on S17 feeder cells in the presence of 1 ug/mL doxycycline.

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CDDP treatment of U2OS cells with NCOR and SMRT knock-down

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