Journal: bioRxiv

Article Title: Transcriptional stochasticity reveals multiple mechanisms of long non-coding RNA regulation at the Xist – Tsix locus

doi: 10.1101/2025.01.05.631290

Figure Lengend Snippet: a Diagram of the Xist/Tsix locus showing Xist exons (green), Tsix exons (magenta), introns (lines), and probe positions for Xist introns (green) and Tsix 3’ introns (magenta). Polymerase positions suggest potential co-transcription of Xist and Tsix. b Conceptual diagram showing expected outcomes with or without TI. If TI occurs, Xist (green) and Tsix 3’ (magenta) signals won’t colocalize (left). Without TI, colocalization occurs (right). c Example image showing DAPI (blue), Xist (green), Tsix 3’ (magenta), and colocalization (white). d-f Similar diagrams and images as (A-C), but for Tsix 5’. With TI, more Xist and Tsix 5’ colocalization occurs than with Tsix 3’ (left); without TI, colocalization remains consistent (right). g-h Joint probability distributions of nascent Tsix (x-axis) and Xist (y-axis) transcripts. Real data is on the left, randomized data on the right. Rho and p values indicate Spearman correlations (real data) and 2D KS test results (randomized data). Analysis includes 625 cells for Tsix 5’ and 651 cells for Tsix 3’. i-n Quantification of colocalization at transcription sites, varying by nascent transcription levels (low, medium, high). Colocalization is plotted by search radius (x-axis, cubic scale) and average events per transcription site (y-axis). Solid line is the mean and shaded area is the standard deviation. Dashed lines is the background fit. Dotted line is the colocalization by chance. i, k, m Quantification of colocalization of Xist with Tsix 3’ depending on the nascent transcription of Xist. Low-level nascent Xist (i), shows colocalization with Tsix 3’ (18 tsites). A greater fraction of medium-level Xist colocalizes with Tsix 3’ (54 tsites) (k), and a lower fraction of high-level Xist colocalizes with Tsix 3’ (11 tsites) (m). A total of n = 651 cells are quantified in this analysis. j, l, n Quantification of colocalization of Xist with Tsix 5’ depending on the nascent transcription of Xist. Low-level nascent Xist (j), shows colocalization with Tsix 5’ (30 tsites). A greater fraction of medium-level Xist colocalizes with Tsix 5’ (68 tsites) (l), and similarly high fraction of high-level Xist colocalizes with Tsix 5’ (33 tsites) (n). A total of n = 625 cells are quantified in this analysis.

Article Snippet: Fluorescent signal was imaged with Semrock Brightline filters for DAPI (DAPI-5060C-NTE-ZERO), CY5 (NIK-0013 RevA-NTE-ZERO), TAMRA (SpGold-B-NTE-ZERO), and AF488 (FITC-2024B-NTE-ZERO).

Techniques: Standard Deviation

Journal: Data in Brief

Article Title: Single molecule mRNA fluorescent in situ hybridization combined with immunofluorescence in S. cerevisiae: Dataset and quantification

doi: 10.1016/j.dib.2020.105511

Figure Lengend Snippet:

Article Snippet: How data were acquired , Data were acquired using a wide-field fluorescence microscope coupled to a CCD camera, a motorized stage driven by ultrasonic piezo technology for precise Z-positioning and a 120 W mercury short arc lamp as fluorescence illumination system. Model and make of the instruments used: Olympus BX-63 epifluorescence microscope equipped with Ultrasonic stage and UPlanApo 100 ×, 1.35NA oil-immersion objective (Olympus). An X-Cite 120 PC Lamp (EXFO), an ORCA-R2 Digital Interline CCD Camera (C10600-10B; Hamamatsu; 6.45 µm-pixel size) mounted using U-CMT and 1X-TVAD Olympus c-Mount Adapters, and zero-pixel shift filter sets: DAPI-5060C-Zero, FITC-5050-000, Cy3-4040C-Zero, and Cy5-4040C-Zero from Semrock. Software used for instrument control and image acquisition: MetaMorph (Molecular Devices)..

Techniques: Expressing, Imaging, Fluorescence, Microscopy, Software, Staining, Immunofluorescence