Journal: EMBO Reports

Article Title: The proximity-based protein interactome and regulatory logics of the transcription factor p65 NF-κB/RELA

doi: 10.1038/s44319-024-00339-8

Figure Lengend Snippet: Reagents and tools table

Article Snippet: The DNA was sheared in 1 ml milliTUBE AFA Fiber (Covaris #520135) by focused-ultrasonicator Covaris S220x (Peak Power 140.0, Duty Factor 5.0, Cycles/Burst 200, Duration 15 min, 4 °C) and lysates were cleared by centrifugation at 16,300× g at 4 °C for 15 min. Supernatants from cleared lysates were collected and stored in aliquots at −80 °C.

Techniques: CRISPR, Bacteria, Recombinant, Clone Assay, Mutagenesis, Control, Plasmid Preparation, Sequencing, Luciferase, Expressing, Labeling, Binding Assay, Modification, Saline, Western Blot, Transfection, Protease Inhibitor, Random Hexamer Labeling, Reverse Transcription, Membrane, In Situ, Proximity Ligation Assay, SYBR Green Assay, Microarray, Software

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Yeast Mitochondrial Transcriptomics

doi: 10.1007/978-1-59745-365-3_35

Figure Lengend Snippet: The distribution of mitochondrial location analyses can be skewed. (A) Example of distribution of the Cy5/Cy3 fluorescence ratios (Rf) that can be obtained from a standard global gene expression experiment. Both repressed and activated genes are expected; the distribution is similar to a normal distribution. (B) Example of distribution of Rf that can be obtained from microarray experiments comparing total RNAs and mitochondria-associated RNAs. Only RNAs enriched in the Cy5 channel are expected: the distribution is skewed by enriched RNA.

Article Snippet: 2.4 Labeled Complementary DNA Synthesis for Microarray Analyses Mastercycler personal (Eppendorf).

Techniques: Fluorescence, Gene Expression, Microarray