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Decode

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DECODE is a lab equipment product by Qiagen. It is a device designed for the analysis and processing of DNA and RNA samples. The core function of DECODE is to facilitate the extraction, purification, and preparation of nucleic acid samples for further downstream applications such as sequencing or detection.

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Lab products found in correlation

Chip it high sensitivity kit, by Active Motif (2 mentions) Epishear multi sample sonicator, by Active Motif (2 mentions) Ab31333, by Abcam (2 mentions) Sc 2025, by Santa Cruz Biotechnology (2 mentions)

3 protocols using decode

1

Steroid Regulation of tPA Expression

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Example 8

Results.

The probability that PLATexpression is directly modulated by steroid is supported by the fact that the PLATgene has multiple transcription factor binding sites. Bioinformatic analysis (DECODE—SABiosciences) reveals that both the human and mouse PLAT genes have binding sites for the glucocorticoid receptors (GR) (alpha and beta), AP1, CREB and NF-KappaB (all reported to act with GR to cause gene repression) within the genomic interval of 20 kB upstream and 10 kb downstream of the gene start codon, suggesting that such direct regulation is possible. In experiments in HTM cells from two donors, the inventors detected PLAT expression downregulation as early as 1 hour after prednisolone administration (FIG. 8). Thus, steroid treatment downregulates tPA. In addition, tPA downregulation represents a biomarker for the development of steroid-induced IOP elevation.

In addition, an additional study on HTM cells indicates that steroid regulation of PLAT is dependent on the first 800 bases proximal to the ATG site of PLAT (FIG. 9).

US11478536B2. Glaucoma treatment (2022-10-25). The Research Foundation for The State University of New York [US], Icahn School of Medicine at Mount Sinai [US]. Inventors: Ioannis Danias [US], Oscar A. Candia [US], Rosana Gerometta [AR].
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2

ChIP-qPCR analysis of p53 binding

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Cardiac fibroblasts (30×106) were fixed in 1% formaldehyde, lysed in lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease inhibitor cocktail Set I CALBIOCHEM) and sonicated using a EpiShear™ Multi-Sample Sonicator (Active Motif), leading to fragments between 300 and 1000 bp. ChIP was performed using a commercially available ChIP-IT High Sensitivity Kit (Active Motif) according to manufacturer’s instructions. DNA-bound protein was immunoprecipitated using an anti-p53 antibody (Catalog#ab31333, Abcam) and anti IgG (Catalog#SC-2025, Santa Cruz) as a negative control. The DNA recovered was analyzed by quantitative real time-PCR using different primers sets that amplified the promoter region of Hoxa9, Hoxd3, CLDNS, Nos3 and negative control genes:
Primers for p53 binding were designed using the SABiosciences’ proprietary database (DECODE, DECipherment Of DNA Elements). Available from: http://www.sabiosciences.com/chipqpcrsearch PCR was performed with equal amounts of specific antibody immunoprecipitated sample, control (IgG) and Input. Values were normalized to input measurements and enrichment was calculated using the comparative Delta-DeltaCt (ΔΔCt) method. Data shown correspond to one representative assay (i.e. 3 PCRs) from a total of 3 independent assays each run with different sets of treated cells.
Ubil E., Duan J., Pillai I.C., Rosa-Garrido M., Wu Y., Bargiacchi F., Lu Y., Stanbouly S., Huang J., Rojas M., Vondriska T.M., Stefani E, & Deb A. (2014). Mesenchymal-endothelial-transition contributes to cardiac neovascularization. Nature, 514(7524), 585-590.
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3

ChIP-qPCR analysis of p53 binding

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Cardiac fibroblasts (30×106) were fixed in 1% formaldehyde, lysed in lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease inhibitor cocktail Set I CALBIOCHEM) and sonicated using a EpiShear™ Multi-Sample Sonicator (Active Motif), leading to fragments between 300 and 1000 bp. ChIP was performed using a commercially available ChIP-IT High Sensitivity Kit (Active Motif) according to manufacturer’s instructions. DNA-bound protein was immunoprecipitated using an anti-p53 antibody (Catalog#ab31333, Abcam) and anti IgG (Catalog#SC-2025, Santa Cruz) as a negative control. The DNA recovered was analyzed by quantitative real time-PCR using different primers sets that amplified the promoter region of Hoxa9, Hoxd3, CLDNS, Nos3 and negative control genes:
Primers for p53 binding were designed using the SABiosciences’ proprietary database (DECODE, DECipherment Of DNA Elements). Available from: http://www.sabiosciences.com/chipqpcrsearch PCR was performed with equal amounts of specific antibody immunoprecipitated sample, control (IgG) and Input. Values were normalized to input measurements and enrichment was calculated using the comparative Delta-DeltaCt (ΔΔCt) method. Data shown correspond to one representative assay (i.e. 3 PCRs) from a total of 3 independent assays each run with different sets of treated cells.
Ubil E., Duan J., Pillai I.C., Rosa-Garrido M., Wu Y., Bargiacchi F., Lu Y., Stanbouly S., Huang J., Rojas M., Vondriska T.M., Stefani E, & Deb A. (2014). Mesenchymal-endothelial-transition contributes to cardiac neovascularization. Nature, 514(7524), 585-590.
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