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To determine relative transcription rates in the WT and AS5ox lines, a run-on assay was performed.
We performed a nuclear run-on assay using the low concentrations (20 µg/ml) of α-amanitin that inhibit pol II but not pol I and III.
To rule out effects of RNA long-term stability and to quantify transcription rates, a nuclear run-on assay was performed using Br-UTP labeling for detection of nascent RNA [44].
Frataxin was previously shown to be upregulated under −Fe conditions using a nuclear run-on assay (Dolezal et al. 2007).
This group performed a global run-on assay in cells cultured with estradiol for acute time courses (10 40 min).
Furthermore, we analysed whether transcription of these genes is regulated by RORγ using a nuclear run-on assay (Fig 3B and Fig S1E of Supporting information).
(A ) For run-on assay, MCF-7 cells were subjected to siRNA knockdown of MAF1 (KD MAF) or simultaneous knockdown of MAF1 and Pol III for 72 hr (KD P/M).
We then measured the elongation activity of Pol I in a nuclear run-on assay, which measures transcription by RNA polymerase that is already bound to DNA, while preventing recruitment of new polymerase molecules to DNA.
Our approach contrasts with a recently published nuclear run-on assay using direct sequencing of cDNA libraries from immunoaffinity captured Br-UTP labeled nascent RNAs without the accompanying analysis of total RNA levels [21].
To investigate the relationship between transcription and the binding of EAST to chromosomes, we performed a run-on transcription assay by including BrUTP into detergent buffer.
To test if the removal of EAST could lead to a higher transcriptional activity in chromosome bands we performed a run-on transcription assay in easthop7 mutants (Figure 2B).
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