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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Trypanosoma cruzi transfected with TcPUF6, a pumilio like protein

ABSTRACT: Functional genomic characterization of mRNAs associated with TcPUF6, a pumilio-like protein from Trypanosoma cruzi

INSTRUMENT(S): Scanning hardware

ORGANISM(S): Trypanosoma cruzi

SUBMITTER: Christian Probst

PROVIDER: E-MEXP-1355 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of differential gene expression during Metacyclogenesis in 2 developmental stages in T.cruzei

Project description:Evaluation of differential gene expression during the metacyclogenesis process in Trypanosoma cruzi, comparing three stages (epimastigotes, stressed epimastigotes and 24h adhered epimastigotes in differentiation) and using both total and polysomal mRNA.

2006-05-16 | E-MEXP-92 | biostudies-arrayexpress

Transcription profiling of human NIH 3T3 inducible cell line to study the role of PKR in regulating gene expression

Project description:PKR is an interferon induced serine/threonine protein kinase, that is activated by double stranded RNA. PKR plays an important role in the antiviral defense by interferon. In addition to its role in translation, PKR participates in several signaling pathways to transcription. The goal of this experiment is to study the role of PKR in regulating gene expression in our NIH 3T3 inducible cell line, which could overexpress PKR wt protein after the removal of tetracycline (Donze O, Dostie J, Sonenberg N. (1999) Virology 256: 322-9).

2004-01-30 | E-MEXP-50 | biostudies-arrayexpress

CTCF binding polarity determines chromatin looping [ChIP-seq]

Project description:CTCF binding polarity determines chromatin looping CTCF ChIPseq was performed in E14 embryonic stem cells and neural precursor cells

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Transcription profiling of human Hep3B cells transfected with L1CAM

Project description:To compare the transcription profiling between empty vector transfected Hep3B and L1CAM transfected Hep3B

2011-08-01 | E-MEXP-1357 | biostudies-arrayexpress

Transcription profiling of mouse neural stem cell lines overexpressing Nurr1 to clonal controls

Project description:The orphan nuclear receptor Nurr1 has been shown to be critical for the development of ventral midbrain dopaminergic neurons. Consequently, the development of ES cells overexpressing Nurr1 has raised hope for the development of cell replacement therapies for Parkinson's Disease to replace degenerated dopaminergic neurons. However, the molecular consequences of Nurr1 on gene expression in these cells remain unknown. To address this, stable, clonal, c17.2 neural stem cell lines were established that overexpressed the orphan nuclear receptor Nurr1 (clone 42 & clone 48) or parental control cell line (puroB & puroD, respectively). Experiment Overall Design: Stable neural stem cell lines were grown in proliferating conditions and matched for further microarray analysis based on their similar proliferation rates: Experiment Overall Design: clone 42(c42) vs. puroB(pB) Experiment Overall Design: clone 42(c48) vs. puroD(pD)

2008-06-12 | E-GEOD-3571 | biostudies-arrayexpress

Transcription profiling of mouse tet inducible NIH 3T3 cells expressing ATPase-defective BRG-1 to identify SWI-SNF-Regulated Genes

Project description:NIH 3T3 cells (mouse fibroblasts) were engineered such that the dominant negative ATPase-defective BRG-1 is expressed via the tet-off inducible expression system to inactivate the SWI-SNF chromatin remodeling complexes (Mol Cell Biol 20, 2839). These cell lines have been used for several studies to demonstrate the in vivo functions of the SWI-SNF complexes in transcription, differentiation and cell cycle control. We used one of those cell line designated as B05-1. B05-1 cells were cultured in the medium with tetracycline for routine maintenance, and cultured in the medium without tetracycline for four days to maximally induce the expression of the dominant negative BRG-1, which we designated as B05-1(+tet) and B05-1(-tet) cells, respectively. The aim of our microarray experiments was to determine the genes whose expression levels are changed by inactivation of the SWI-SNF complexes by analyzing the genes differentially expressed between B05-1(+tet) and B05-1(-tet) cells. It should be noted that, since the comparison was made between B05-1 cells cultured with and without tetracycline for four days, the genes differentially expressed between these two cells do not only represent the genes that are directly regulated by the SWI-SNF complexes but also include the genes that are secondarily affected by SWI-SNF inactivation as well as the genes whose expression is changed by tetracycline effect per se.

2006-01-01 | E-MEXP-434 | biostudies-arrayexpress

CTCF binding polarity determines chromatin looping

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-10-29 | E-GEOD-72720 | biostudies-arrayexpress

Transcription profiling of wild type mice stomach and colon samples

Project description:Comparison of stomach and colon in normal mice.

2006-08-16 | E-MEXP-402 | biostudies-arrayexpress

Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C

Project description:Small, non-coding RNAs control gene expression post-transcriptionally and play important roles in virus-host interactions. Within the liver, the microRNA (miRNA) miR-122 is essential for replication of hepatitis C virus (HCV), while repression of miR-148a by hepatitis B virus (HBV) may enhance tumorigenesis. Despite their importance to the outcome of these infections, few previous studies have described unbiased profiling of small RNAs in the liver during chronic viral hepatitis. Here, we sequenced small (14-40 nts) RNAs in liver from subjects with chronic hepatitis B and C. We found that small RNAs derived from tRNAs, specifically 5’ tRNA-halves (“5’ tRHs”, ~31-34 nts), are abundant in liver and significantly increased during chronic viral infection in humans and also chimpanzees. In most infected livers, 5’ tRH abundance exceeded that of miRNAs. In contrast, in hepatocellular carcinoma (HCC) tissue from these subjects, tRH abundance was reduced concomitant with decreased expression of the tRNA-cleaving ribonuclease, angiogenin. Although tRHs have been identified in mice, our results show they are abundantly expressed in human tissue, increased in chronic viral infection, and decreased in liver cancer. Our findings highlight the potential biological and clinical relevance of these small non-coding RNAs. Small RNA-seq of liver samples from control subjects (n=4), subjects with chronic hepatitis B (n=4) and hepatitis B associated hepatocellular carcinoma (n=4, 3 out of 4 matched with non-tumor tissue) and subjects with chronic hepatitis C (n=4) and tissue from hepatocellular carcinoma of the same patients. Also, small RNA-seq of AGO2 and IgG pulldown in FT3-7 cells. Sequenced AGO2 pulldown (n=3), IgG pulldown (n=2) and total small RNA from FT3-7 cells (n=3). This dataset is part of the TransQST collection.

2014-12-18 | E-GEOD-57381 | biostudies-arrayexpress

RAD54L2 mediates a novel mechanism to counter TOP2-DNA adducts

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2024-01-26 | PXD046611 | Pride

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