RTPrimerDB: the Real-Time PCR primer and probe database

Pattyn, Filip

doi:10.1093/nar/gkg011

Cited by 223 publications

(138 citation statements)

References 13 publications

Supporting

Mentioning

137

Contrasting

Unclassified

Order By: Relevance

“…The primer sequences were as follows (sense and antisense, respectively): interleukin 2 (IL2): 5-TCCCAAACTCACC AGGATGCTCACA-3, 5-GCACTTCCTCCAGAGGTTTG AGTTCT-3; interleukin 17A (IL17A): 5-TTCCCCCG GACTGTGATGGT-3, 5-CGGCACTTTGCCTCCCAG AT-3; guanylate-binding protein 1, interferon-inducible (GBP1): 5-TCCCAGCCCTACAACTTCGG-3, 5-TGCCA TGTCCAGGCTGTTCC-3. The primer sequences for interleukin 2 receptor a (IL2RA), chemokine (C-X-C motif) ligand (CXCL) 11, ubiquitin D (UBD), tumor necrosis factor receptor superfamily member 9 (TNFRSF9), interferon c (IFN-c) and CXCL9 have been previously described (Nishioka et al 2007;Pattyn et al 2003;Spandidos et al 2008;Wang and Seed 2003).…”

Section: Qrt-pcrmentioning

confidence: 99%

See 1 more Smart Citation

Lactobacillus paracasei and Lactobacillus plantarum strains downregulate proinflammatory genes in an ex vivo system of cultured human colonic mucosa

et al. 2012

View full text Add to dashboard Cite

Significant health benefits have been demonstrated for certain probiotic strains through intervention studies; however, there is a shortage of experimental evidence relative to the mechanisms of action. Here, noninvasive experimental procedure based on a colon organ culture system has been used that, in contrast to most experimental in vitro models reported, can preserve natural immunohistochemical features of the human mucosa. This system has been used to test whether commensal lactobacilli (Lactobacillus paracasei BL23, Lactobacillus plantarum 299v and L. plantarum 299v (A -)) were able to hinder inflammation-like signals induced by phorbol 12-myristate 13-acetate (PMA)/ionomycin (IO). Whole genome microarrays have been applied to analyze expression differences, from which mRNA markers could be inferred to monitor the effect of putative probiotic strains under such conditions. Regarding the gene expression, PMA/IO treatment induced not only interleukin (IL)-2 and interferon gamma (IFN-c), as expected, but also other relevant genes related to immune response and inflammation, such as IL-17A, chemokine (C-X-C motif) ligand (CXCL) 9 and CXCL11. The ex vivo culturing did not modify the pattern of expression of those genes or others related to inflammation. Interestingly, this study demonstrated that lactobacilli downregulated those genes and triggered a global change of the transcriptional profile that indicated a clear homeostasis restoring effect and a decrease in signals produced by activated T cells.

show abstract

Section: Qrt-pcrmentioning

confidence: 99%

“…Reactions were performed in triplicate, and relative quantification of gene expression was achieved using the efficiency-corrected method according to Pfaffl (2001). Primer sequences of the housekeeping genes ACTB, GAPDH, HPRT1, RPL13A, SDHA, B2M and YWHAZ were used as reported elsewhere (Chiu et al 2005;Pattyn et al 2003). …”

Section: Qrt-pcrmentioning

confidence: 99%

Lactobacillus paracasei and Lactobacillus plantarum strains downregulate proinflammatory genes in an ex vivo system of cultured human colonic mucosa

et al. 2012

View full text Add to dashboard Cite

show abstract

“…wiley.com/jpages/1058-8388/suppmat), and additional information is available online in the primer database: RTPrimerDB (Pattyn et al, 2003; http://medgen.Ugent.be/rtprimerdb).…”

Section: Primer Design and Testingmentioning

confidence: 99%

Expression of all Wnt genes and their secreted antagonists during mouse blastocyst and postimplantation development

Kemp

Willems

Abdo

et al. 2005

Developmental Dynamics

200

158

View full text Add to dashboard Cite

In this extensive study, real-time reverse transcriptase-polymerase chain reaction was used to analyze the expression levels of all 19 Wnt genes and their 11 potential antagonists in mouse blastocysts, pregastrula, gastrula, and neurula stages. By complementing these results with in situ hybridization, we revealed new expression domains for Wnt2b and Sfrp1, respectively, in the future primitive streak at the posterior side and in the anterior visceral endoderm before the initiation of gastrulation. Moreover, the anterior visceral endoderm expresses three secreted Wnt antagonists (Sfrp1, Sfrp5, and Dkk1) in partially overlapping domains. We also identified expression patterns for the Wnt1, Wnt3a, Wnt6, Wnt7b, Wnt9a, Wnt10b, and Sfrp1 genes at the blastocyst stage. In particular, the expression of Wnt1 and Sfrp1 predominantly in the inner cell mass and of Wnt9a in the mural trophoblast and inner cell mass cells surrounding the blastocoele suggests new roles for the Wnt pathway in preimplantation development. This article is the first report on the regional expression of Wnt genes in the mouse blastocyst.

show abstract

“…Realtime qPCR was performed using the cDNA equivalent of 25 ng total RNA, 330 nM of each primer and 12.5 ml SYBR Green PCR Master Mix (Applied Biosystems, Foster City, CA, USA) in a total volume of 25 ml. MEIS1 (ID3185) primer sequences were taken from the RTprimerDB (Pattyn et al, 2003), POLR2A primers were provided by E Korpershoek and S100A8 primer sequences were 5 0 -ATG TTG ACC GAG CTG GAG AA-3 0 and 5 0 -CAG AAT GAG GAA CTC CTG GAA G-3 0 . Standards were prepared by fourfold serial dilutions of a pooled sample, consisting of equal amounts of cDNA from each of the MN1-and MN1-TEL-inducible cell lines.…”

Section: Transient Transfectionsmentioning

confidence: 99%

The MN1-TEL myeloid leukemia-associated fusion protein has a dominant-negative effect on RAR-RXR-mediated transcription

et al. 2007

View full text Add to dashboard Cite

The translocation t(12;22)(p13;q11) creates an MN1-TEL fusion gene leading to acute myeloid leukemia. MN1 is a transcription coactivator of the retinoic acid and vitamin D receptors, and TEL (ETV6) is a member of the E26-transformation-specific family of transcription factors. In MN1-TEL, the transactivating domains of MN1 are combined with the DNA-binding domain of TEL. We show that MN1-TEL inhibits retinoic acid receptor (RAR)-mediated transcription, counteracts coactivators such as p160 and p300, and acts as a dominant-negative mutant of MN1. Compared to MN1, the same transactivation domains in MN1-TEL are poorly stimulated by p160, p300 or histone deacetylase inhibitors, indicating that the block of RAR-mediated transcription by MN1-TEL is caused by dysfunctional transactivation domains rather than by recruitment of corepressors. The mechanism leading to myeloid leukemia in t(12;22) thus differs from the translocations that involve RAR itself.

show abstract

RTPrimerDB: the Real-Time PCR primer and probe database

Cited by 223 publications

References 13 publications

Lactobacillus paracasei and Lactobacillus plantarum strains downregulate proinflammatory genes in an ex vivo system of cultured human colonic mucosa

Lactobacillus paracasei and Lactobacillus plantarum strains downregulate proinflammatory genes in an ex vivo system of cultured human colonic mucosa

Expression of all Wnt genes and their secreted antagonists during mouse blastocyst and postimplantation development

The MN1-TEL myeloid leukemia-associated fusion protein has a dominant-negative effect on RAR-RXR-mediated transcription

Contact Info

Product

Resources

About