PA_IP_032004_pA
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LCQ DECA
ORGANISM(S): Halobacterium Nrc-1 (halobacterium)
SUBMITTER: Nitin Baliga
PROVIDER: PAe000237 | PeptideAtlas |
REPOSITORIES: PeptideAtlas
Similar Datasets
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Project description:Investigation of whole genome gene expression level changes in a colorectal cancer cell line SW480 expressing FOXC2, compared to the pBabe control cells. Genes associated with metastasis regulated by FOXC2 in colorectal cancer were analysed. The role of FOXC2 in breast cancer metastasis are further described in Mani SA, Yang J et al. Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers. PNAS 2007; 104: 10069-10074 .
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Project description:Huh7/5-2 cells (Binder et al., Hepatology 2007) were mock infected (DMEM) (time points 4 and 48 h) or infected with the chimeric HCV virus Jc1 (Pietschmann et al., PNAS 2006) (all time points). Multiplicity of infection was 15 (TCID50). Cells were lysed after 4, 12, 24, 48 and 72 hours post infection and total cellular RNA was prepared. Mock infected cells serve as controls for the infected samples. The whole experiment was repeated on independent days (2 biological replicates). The dataset was also submitted to GEO (GSE38720).
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Project description:The critical role of the endothelium in governing vascular, tissues homeostasis and pathological processes is increasingly recognized (Deanfield et al., 2007). Cellular senescence of endothelial cells has been proposed to be involved in endothelial dysfunction and atherogenesis (Minamino T et al., 2007), although the mechanisms underlying the aging induced attenuation of endothelium dependent functions are yet to be clarified. Recent evidences implicated overall miRNA levels and miRNA in regulating angiogenesis and endothelial function (Suarez et al., 2007; Kuehbacher et al., 2007; Harris et al., 2008; Fish et al. 2008; Wang et al., 2008).
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Project description:Investigation of whole genome gene expression level changes in a colorectal cancer cell line SW480 expressing FOXC2, compared to the pBabe control cells. Genes associated with metastasis regulated by FOXC2 in colorectal cancer were analysed. The role of FOXC2 in breast cancer metastasis are further described in Mani SA, Yang J et al. Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers. PNAS 2007; 104: 10069-10074 . A six chip study using total RNA recovered from three separate cultures of SW480/pBabe and three separate cultures of SW480/FOXC2. Each chip measures the expression level of 45033 genes from SW480/pBabe or SW480/FOXC2.
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Project description:We used the Virochip microarray to detect and discover a novel adenovirus, TMAdV (titi monkey adenovirus). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes, of which 19,058 probes are 70-mer viral oligonucleotides (the union of the V3 and V4 platforms -- please see Wang, et al., PNAS, 2002; Chiu, et al., Clin Infect Dis, 2006; Chiu, et al., PNAS, 2008).
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Project description:Several studies indicate that plant MIR genes are transcribed by RNA Pol II, similar to what is found in animals (Cai et al., 2004; Lee et al., 2004). By sequencing the 5' transcript ends Xie et al. (2005) mapped the transcription start sites (TSSs) for 52 MIR genes. This list was expanded upon through computational prediction of the core promoters (Zhou et al., 2007). In addition to the TATA box sequence motifs located upstream of the TSSs (Xie et al. 2005), Megraw et al. (2006) identified other transcription factor binding motifs in the promoter of Arabidopsis MIR genes. They showed that within the 800 nucleotides region upstream of TSSs, sequences resembling the binding sites for the transcription factors AtMYC2, ARF, SORLREP3, and LFY were overrepresented relative to protein-coding gene promoters and randomly sampled genomic sequences (Megraw et al. 2006). While these previous studies are instrumental in establishing our working understanding of MIR gene transcription in plants, there are several major knowledge gaps that urgently need to be addressed. Binding of RNA Pol II to the identified MIR promoter regions has not been tested. Because expression of MIR genes does not involve translation, transcriptional control by RNA Pol II might be different from protein-coding genes. In addition, few of the predicted cis elements have been functionally tested. Futher, the number of annotated miRNA genes has since increased from 199 to 232 (miRBase release 17; Kozomara and Griffiths-Jones, 2011). None of the newly identified genes have been subject to examination for promoter and regulatory sequences. Compared to the previously known miRNAs, these genes have narrower phylogenetic distribution and exhibit weaker expression level and more prominent tissue-specific expression (Rajagopalan et al., 2006; Fahlgren et al. 2007; Yang et al., 2011). Based on these observations, it has been argued that continuous gene birth and death allows beneficial miRNAs to be maintained while deleterious ones avoided (Rajagopalan et al., 2006; Fahlgren et al. 2007; Chen and Rajewsky, 2007; Axtell and Bowman, 2008). Identification of the promoter regions of these MIR genes and their comparison to those of the conserved are highly desirable to fully elucidate miRNA based gene regulation. In the current study, we performed chromatin immunoprecipitation (ChIP)-chip for the Pol II complex using the Affymetrix 'At35b_MR_v04' array. We designed a computational approach using genome-wide RPol II binding patterns to identify the promoter region and transcription start site of pri-miRNAs that are actively transcribed.
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