Journal: bioRxiv

Article Title: Spatial 5mC-seq profiling of embryos and decidua after implantation in mammal

doi: 10.64898/2025.12.15.694289

Figure Lengend Snippet: a , Schematic designs of the three versions of microchannel chips used in this study. b , Genome coverage of SmC-seq at the pseudobulk level under three different HCl treatment conditions. “3× HCl” indicates treatment with 0.2 N HCl at room temperature for 5 min per round, repeated for three rounds; “1× HCl” indicates a single round of the same treatment; “No HCl” indicates no HCl treatment. “Rep” denotes replicate. For each of the six samples, 69,256,892 raw reads were used as input. Genome coverage was defined as the proportion of CpGs across the whole genome that were covered by sequencing reads. c , Fluorescent imaging measuring cross-channel diffusion distances and possible crosstalk between two neighboring channels by alternately flowing 5-Carboxyfluorescein (5-FAM, Green)-labeled Barcode A and Cyanines3 (Cy3, Red)-labeled Barcode A in adjacent channels. E5.5 embryonic tissue sections, with or without three-rounds of HCl treatment, were evaluated and compared. The microchannel chip used here consists of 10 μm width channels with 5 μm spacing. d , Quantification of diffusion distances with and without three-rounds of HCl treatment. Two-side t-test was used for statistical analysis.

Article Snippet: For each channel, 3 μL of RNA barcode buffer (1.8x T4 Ligase buffer, 30 U/μL T4 DNA Ligase, 0.75x NEB Buffer 3.1, 0.2% Triton-X100, 5 U/μL RNase Inhibitor (Enzymatics), and 0.1 U/μL SUPERase•InTM RNase Inhibitor) and 1 μL of RNA barcode A were added.

Techniques: Sequencing, Imaging, Diffusion-based Assay, Labeling

Journal: The Journal of Infectious Diseases

Article Title: Immune Reconstitution Bone Loss Exacerbates Bone Degeneration Due to Natural Aging in a Mouse Model

doi: 10.1093/infdis/jiab631

Figure Lengend Snippet: Quantification of gene expression patterns of inflammatory and osteoclastogenic cytokines in purified CD4+ T cells in mice at 20 months of age. CD4+ T cells were immunomagnetically purified from spleens of 20-month-old wild-type (WT) C57BL6/J and T-cell-reconstituted TCRβ knockout (KO) mice (T cells) and subjected to NanoString mRNA gene quantification for common osteoclastogenic and inflammatory cytokines: (A) mRNA for downstream osteoclastogenic mediators (RANKL, osteoprotegerin, and the RANKL/osteoprotegerin ratio). (B) Inflammatory mediators of osteoclastogenesis (tumor necrosis factor [TNF]α and IL-1β) and (C) IL-17A and IL-6. Data are expressed as boxplots (median ± interquartile range) with 10 to 90 percentile whiskers: ∗P < .05 and ∗∗P < .01 by Mann-Whitney U test. Nonsignificant comparisons not shown. n = 5 WT and 7 T-cell mice/group.

Article Snippet: Expression of RANKL, OPG, TNFα, interleuking (IL)-1β, IL-17A, and IL-6 messenger ribonucleic acid (mRNA) was quantified from 50 000 immunomagnetically purified (StemCell Technologies) CD4 + T cells lysed directly in 1:3 RLT buffer (QIAGEN, Germantown, MD) and hybridized with gene-specific fluorescent barcoded probes at 65°C for 24 hours without RNA extraction.

Techniques: Gene Expression, Purification, Knock-Out, MANN-WHITNEY