Mus musculus
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ABSTRACT:
PROVIDER: PRJNA171031 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Gene expression in the top, light and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples This study was performed to examine whether the expression of certain genes in LNSCs is regulated by the translation factor, eukaryotic translation initiation factor 4 gamma 3 (Eif4g3).
2011-09-01 | GSE29152 | 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:Gene expression in the top, light and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples This study was performed to examine whether the expression of certain genes in LNSCs is regulated by the translation factor, eukaryotic translation initiation factor 4 gamma 3 (Eif4g3). LNSCs were grown in 10 cm plates, allowed to reach ≥ 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. Cells were pooled, lysed and fractionated on a 10% to 60% continuous sucrose gradient. Fractions were collected and pooled into the top, light and heavy polysome fractions. RNA was extracted from these samples and used for microarrays on the Agilent Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays.
2011-08-31 | E-GEOD-29152 | biostudies-arrayexpress
Project description:Lymph node stromal cells: Control siRNA treated vs. Eif4g3 siRNA treated
| PRJNA142983 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE29152: Lymph node stromal cells: Control siRNA treated vs. Eif4g3 siRNA treated GSE29153: Differential gene expression in the Pancreatic lymph node of Deaf1 knockout mice vs. wild type littermate controls Refer to individual Series
2011-08-31 | E-GEOD-29167 | biostudies-arrayexpress
Project description:Purpose: In this study, we have used a translatomic approach by coupling polysome profiling and deep RNA-sequencing to estimate changes in the translatome of antimony-resistant Leishmania parasites Methods: Leishmania tropica promastigotes were stepwise selected for resistance to trivalent antimony. Two different strains were studied, the L. tropica SbIII-sensitive or wildtype strain (WT) and the derived highly resistant strain (HR). After polysome profiling four types of samples were evaluated by deep RNAseq: total mRNA used as input, monosomes (MS), light polysomes (LP), and heavy polysomes (HP). The DESeq2 algorithm was used for differential expression analysis to identify translational changes at the basal level (HR Vs. WT), translational changes to combat the drug (HR+SbIII Vs. HR), and to compare translatomic Vs. transcriptomic changes (HP Vs. Total input) [see overall design section below]. Results: Differential translational analysis (cutoff of fold change ≥ 1.5 and p-value corrected by Benjamini-Hochberg FDR ≤ 0.05) showed that transcripts composition per polysome fraction was different in the resistant strain. It included several upregulated (Up) and downregulated (Down) transcripts. At the basal level, 2431 different transcripts were differentially translated: monosome (Down: 4, Up: 0), light polysomes (Down: 906, Up: 951), and heavy polysomes (Down: 1096, Up: 1064). Under the antimony challenge, 189 different transcripts were differentially translated: monosome (Down: 0, Up: 2), light polysomes (Down: 9, Up: 57), and heavy polysomes (Down: 30, Up: 134). Overall, most of the changes were identified in polysome fraction when compared with monosomes or total transcriptome. Conclusions: Our study shows evidence that translational control has a main role in coordinating the resistance to antimony in Leishmania parasites. We propose a novel model that establishes translational control as a major driver of antimony-resistant phenotypes in Leishmania parasites.
2023-04-04 | GSE173848 | GEO
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:Comparison of total RNA isolated from ASML and ASML CD44v knockdown exosomes; and RNA from untreated B12 lymph node stroma cells vs. cells treated for 24h with ASML wt or ASML CD44v kd exosomes
2011-12-28 | GSE34737 | GEO
Project description:Tissue structure of the lymph node (LN) is supported by the network of stromal cells of mesenchymal origin, which is suggested to contribute to various immunological processes. In order to identify stromal cellM-bM-^@M-^Sderived factors that regulate immune function, we performed gene expression profiling of stromal cells freshly isolated from collagenase digested mouse LNs, cultured stromal cell lines, and embryonic fibroblasts as a mesenchymal control. Total RNAs extracted from the CD45-CD31-podoplanin+VCAM-1+ stromal cell fraction was sorted from enzymatically digested mouse LNs, cultured stromal cell lines stimulated with or without lymphotoxin (LTM-NM-2R agonistic antibody), and mouse embryonic fibroblasts (MEFs) were used for microarray analysis to assess relative gene expression.
2014-06-19 | E-GEOD-55251 | biostudies-arrayexpress