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All cells were maintained at 37°C and 5% CO2 Nuclear preparations were prepared as previously described [ 25].
(f h) Subgroup assignment and probability estimates (dots) along with 95% confidence intervals (boxplots) for 101 medulloblastoma samples for which DNAs were derived from three types of materials: Fresh frozen biopsies (n = 40), formalin-fixed paraffin-embedded biopsies (FFPE, tumour section; n = 35) and FFPE-derived cytospin nuclear preparations (n = 26).
In total, this resulted in three 14N liver/15nuclear nuclear preparations and three 14N brain/15N liver.
Tubulin, cyclin A and histone H1 expression were used as controls to identify the purity of cytoplasmic and nuclear preparations, respectively.
Total RNA was purified from nuclear preparations of S2 cells that expressed either the wt or the mut β-globin genes and this RNA was reverse-transcribed.
Subcellular localization studies were performed on kidney because of the relative abundance of the transgenic product in kidney, the ability to obtain adherent cells for fluorescence microscopy and the ability to obtain quality nuclear preparations.
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Nuclear preparation buffer (SXN), TN (Tris/NaCl buffer) and egg lysis buffer [10] were prepared as described previously [11].
The purity of the nuclear preparation was checked by probing it with an anti-β-tubulin antibody that detected tubulin in the cytoplasmic fraction only indicating that the nuclear preparation was free from cytoplasmic proteins (Figure 2A, right panel).
Verification of the purity of this nuclear preparation by western blot analysis has been previously published [28].
Each nuclear preparation was sampled four times.
Our nuclear preparation contained 99% intact nuclei.
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