Cytoplasmic mRNA and Heavy polysome-associated mRNAs from U251 Cells treated with Control or eIF3e siRNAs
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PROVIDER: PRJNA662223 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptional profiling of Cytoplasmic mRNA and Heavy polysome-associated mRNAs extracted from U251 Cells treated with control siRNA or siRNA targeting eIF3e . Goal was to determine the effect of eIF3e knockdown on translation of specific mRNAs.
2020-09-09 | GSE157608 | GEO
Project description:Gene expression in the total RNA and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples The objective of this study was to identify genes whose translation are reduced after silencing Eif4g3 (the gene which encodes the translation initiation factor eIF4GII). Genes with reduced translation are expected to have lower expression in RNA samples isolated from heavy polysomes but not in RNA samples isolated from whole cell lysates. LNSCs were grown in 10 cm plates, allowed to reach M-bM-^IM-% 80% confluency and then transfected with 400 pmol of control or Eif4g3 siRNA using Lipofectamine 2000. 7 plates were transfected with control or Eif4g3 siRNA. Total RNA was extracted from cells 48h after transfection. To isolate RNA from the heavy polysome fractions, cells were pooled, lysed and fractionated on a 10% to 60% continuous sucrose gradient. Fractions containing the heavy polysome fractions were pooled. RNA was extracted from these samples and used for microarrays on the Agilent Whole Mouse Genome Microarray Kit, 4M-CM-^W44K 2-color arrays.
2012-07-19 | E-GEOD-39408 | biostudies-arrayexpress
Project description:RNA helicase A (RHA) binds its target transcripts at the post-transcriptional control element (PCE) located in the 5â?? untranslated region (UTR). This interaction represents an â??RNA switchâ?? that regulates protein synthesis. Down regulation of RHA by siRNAs was used to identify transcripts with RHA-dependent translation. Reduced accumulation of RNA in polysomes was monitored with microarrays. Changes in cytoplasmic RNA steady state abundance was monitored as well. Sixty nine genes exhibit decreased transcript polysome association when subjected to RHA downregulation. A majority of the transcripts that experienced a reduction in the polysome fraction had no significant change in their cytoplasmic abundance (45 genes). Keywords: gene expression array-based Cytoplasmic lysates of cells treated with RHA targeted or non-silencing control siRNAs were separated by sucrose density gradient centrifugation. Ribosomal RNA profiles were generated, fractions containing polysomes were collected, and RNA was extracted.
2010-05-15 | E-GEOD-14055 | biostudies-arrayexpress
Project description:Gene expression in the total RNA and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples The objective of this study was to identify genes whose translation are reduced after silencing Eif4g3 (the gene which encodes the translation initiation factor eIF4GII). Genes with reduced translation are expected to have lower expression in RNA samples isolated from heavy polysomes but not in RNA samples isolated from whole cell lysates.
2012-07-20 | GSE39408 | GEO
Project description:RNA helicase A (RHA) binds its target transcripts at the post-transcriptional control element (PCE) located in the 5’ untranslated region (UTR). This interaction represents an “RNA switch” that regulates protein synthesis. Down regulation of RHA by siRNAs was used to identify transcripts with RHA-dependent translation. Reduced accumulation of RNA in polysomes was monitored with microarrays. Changes in cytoplasmic RNA steady state abundance was monitored as well. Sixty nine genes exhibit decreased transcript polysome association when subjected to RHA downregulation. A majority of the transcripts that experienced a reduction in the polysome fraction had no significant change in their cytoplasmic abundance (45 genes). Keywords: gene expression array-based
2008-12-20 | GSE14055 | GEO
Project description:RNA helicase A (RHA) binds its target transcripts at the post-transcriptional control element (PCE) located in the 5’ untranslated region (UTR). This interaction represents an “RNA switch” that regulates protein synthesis. Down regulation of RHA by siRNAs was used to identify transcripts with RHA-dependent translation. Reduced accumulation of RNA in polysomes was monitored with microarrays. Cytoplasmic lysates of cells treated with RHA targeted or non-silencing control siRNAs were separated by sucrose density gradient centrifugation. Ribosomal RNA profiles were generated, containing heavy polysomes were collected, and RNA was extracted.
2010-08-19 | E-GEOD-23669 | biostudies-arrayexpress
Project description:we performed microarray expression profiling to analyze the differentially expressed genes between U251-shCtrl and U251-shCPVL cells.
2024-11-01 | GSE188414 | GEO
Project description:Human histomonocytic U937 cells exhibit macrophage-like properties after phorbol ester stimulation. Accumulating evidence demonstrated that remarkable number of transcripts changed in their amount at total RNA levels. However, post-transcriptional regulation has not been fully elucidated in this model. Thus, we compared expression profiles between polysomal and cytoplasmic RNAs before and after phorbol 12-myristate 13-acetate stimulation (48h, 32nM). Table 1: Detailed description of the expression data of human histomonocytic cell line U937 cells. Data of total cytoplasmic and polysomal fractions before and after PMA stimulation is shown. This table contains all spot data except: 1) saturated spots, 2) undetectable spots, 3) stained spots, and 4) spots only detected in less than one samples. Column A: Gene symbol (âI_xxxxxxâ is corresponding to EST clones); Column B: Genbank accession no. Column C: Description; Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA; Column E: Average value of expression levels in total cytoplasmic fraction in the presence of PMA (32nM, 48h); Column F: Average value of expression levels in polysomal fraction in the absence of PMA; Column G: Average value of expression levels in polysomal fraction in the presence of PMA; Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-); Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+); Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-); Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-); Column L: Different expression between polysome, PMA (-) and cytoplasm, PMA(-): different=1; Column M: Different expression between polysome, PMA (+) and cytoplasm, PMA(+): different=1; Column N: Different expression between cytoplasm, PMA (+) and cytoplasm, PMA(-): different=1; Column O: Different expression between polysome, PMA (+) and polysome, PMA(-): different=1; ; Table 2: Candidates post-transcriptionally regulated by PMA. We extracted 105 transcripts whose expression levels were altered only in either fraction accompanied by changes in polysome/cytoplasm expression ratio. Column A: Gene symbol (âI_xxxxxxâ is corresponding to EST clones); Column B: Genbank accession no. Column C: Description; Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA; Column E Average value of expression levels in total cytoplasmic fraction in the presence of PMA; Column F: Average value of expression levels in polysomal fraction in the absence of PMA; Column G: Average value of expression levels in polysomal fraction in the presence of PMA; Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-); Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+); Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-); Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-)
2008-06-11 | E-GEOD-1783 | biostudies-arrayexpress
Project description:Human histomonocytic U937 cells exhibit macrophage-like properties after phorbol ester stimulation. Accumulating evidence demonstrated that remarkable number of transcripts changed in their amount at total RNA levels. However, post-transcriptional regulation has not been fully elucidated in this model. Thus, we compared expression profiles between polysomal and cytoplasmic RNAs before and after phorbol 12-myristate 13-acetate stimulation (48h, 32nM). Table 1: Detailed description of the expression data of human histomonocytic cell line U937 cells. Data of total cytoplasmic and polysomal fractions before and after PMA stimulation is shown. This table contains all spot data except: 1) saturated spots, 2) undetectable spots, 3) stained spots, and 4) spots only detected in less than one samples. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E: Average value of expression levels in total cytoplasmic fraction in the presence of PMA (32nM, 48h) Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Column L: Different expression between polysome, PMA (-) and cytoplasm, PMA(-): different=1 Column M: Different expression between polysome, PMA (+) and cytoplasm, PMA(+): different=1 Column N: Different expression between cytoplasm, PMA (+) and cytoplasm, PMA(-): different=1 Column O: Different expression between polysome, PMA (+) and polysome, PMA(-): different=1 Table 2: Candidates post-transcriptionally regulated by PMA. We extracted 105 transcripts whose expression levels were altered only in either fraction accompanied by changes in polysome/cytoplasm expression ratio. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E Average value of expression levels in total cytoplasmic fraction in the presence of PMA Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Keywords = phorbol ester Keywords = macrophage Keywords = polysome Keywords = post-transcriptional regulation Keywords: parallel sample
2004-11-01 | GSE1783 | GEO
Project description:To investigate the function of COL8A1 in GSCs progression, we established U251-COL8A1 cell lines with COL8A1 overexpressed. Then we performed gene expression profiling analysis using data obtained from RNA-seq of 2 cells (U251NC and U251-COL8A1)
2024-07-01 | GSE246528 | GEO