Data from: NF-κB oscillations translate into functionally related patterns of gene expression
| العنوان: | Data from: NF-κB oscillations translate into functionally related patterns of gene expression |
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| المؤلفون: | Zambrano, Samuel, De Toma, Ilario, Piffer, Arianna, Bianchi, Marco E., Agresti, Alessandra |
| سنة النشر: | 2016 |
| المجموعة: | Zenodo |
| مصطلحات موضوعية: | mouse embryo fibroblasts, Mus musculus, Pulsed stimulation |
| الوصف: | Several transcription factors (TFs) oscillate, periodically relocating between the cytoplasm and the nucleus. NF-κB, which plays key roles in inflammation and cancer, displays oscillations whose biological advantage remains unclear. Recent work indicated that NF-κB displays sustained oscillations that can be entrained, that is, reach a persistent synchronized state through small periodic perturbations. We show here that for our GFP-p65 knock-in cells NF-κB behaves as a damped oscillator able to synchronize to a variety of periodic external perturbations with no memory. We imposed synchronous dynamics to prove that transcription of NF-κB-controlled genes also oscillates, but mature transcript levels follow three distinct patterns. Two sets of transcripts accumulate fast or slowly, respectively. Another set, comprising chemokine and chemokine receptor mRNAs, oscillates and resets at each new stimulus, with no memory of the past. We propose that TF oscillatory dynamics is a means of segmenting time to provide renewing opportunity windows for decision. ; Microarray data; chronic and pulsed stimulations of TNFalphaGFP-p65 MEFs were either chronically or periodically stimulated (90' and 180' forcing periods) with TNF-alpha. RNA samples were extracted at selected timepoints using the Illustra RNAspin Mini kit (GE Healthcare). Following extraction, RIN (RNA Integrity Number) was >9 (BioAnalyser, Agilent RNA Nano Kit). RNA samples (500 ng) were reverse transcribed with the Illumina TotalPrep RNA Amplification Kit (Ambion) and copy RNA (cRNA) was generated with 14 hour in vitro transcription reactions and checked at the BioAnalyser. Washing, staining, and hybridization were performed according to standard Illumina protocols. cRNA samples were then hybridized to Illumina BeadChip Array MouseRefSeq-8 v2. BeadChips were scanned with BeadArray™ Reader in channel 2. The .zip file contains the following files: Quality control files: "Zambrano_90MIN_ControlProbe.csv", "Zambrano_180MIN_ControlProbe.csv", ... |
| نوع الوثيقة: | dataset |
| اللغة: | unknown |
| العلاقة: | https://zenodo.org/communities/dryadTest; https://zenodo.org/record/4937196Test; https://doi.org/10.5061/dryad.j62n1Test; oai:zenodo.org:4937196 |
| DOI: | 10.5061/dryad.j62n1 |
| الإتاحة: | https://doi.org/10.5061/dryad.j62n1Test https://doi.org/10.7554/eLife.09100Test https://zenodo.org/record/4937196Test |
| حقوق: | info:eu-repo/semantics/openAccess ; https://creativecommons.org/publicdomain/zero/1.0/legalcodeTest |
| رقم الانضمام: | edsbas.40E043EC |
| قاعدة البيانات: | BASE |
| DOI: | 10.5061/dryad.j62n1 |
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