hifi circular consensus dna sequencing libraries  (Pacific Biosciences)

Journal: Environmental Microbiology

Article Title: The Adult Aedes aegypti Bacterial Microbiota is Robust to Infection with the Obligate Microsporidian Parasite Edhazardia aedis

doi: 10.1111/1462-2920.70437

Figure Lengend Snippet: Infection with E. aedis does not alter bacterial load in the abdomens of A. aegypti . The y ‐axis displays log10‐transformed ∆ X 0,16S values, which were obtained from analysis of quantitative PCR data, and represent the starting amount of 16S bacterial DNA in each sample normalized to the amount of RpS7 reference mosquito DNA. ∆ X 0,16S values serve as a proxy for measurement of bacterial load. The p value indicates the result of a mixed linear model testing the effect of E. aedis infection on log10‐transformed ∆ X 0,16S values.

Article Snippet: Amplicons were submitted to NC State Genomic Sciences Laboratory for subsequent library preparation following the Illumina 16S Metagenomic Sequencing Library Preparation guide ( 16S Metagenomic Sequencing Library Preparation: Preparing 16S Ribosomal RNA Gene Amplicons for the Illumina MiSeq System ).

Techniques: Infection, Transformation Assay, Analysis, Real-time Polymerase Chain Reaction

Journal: bioRxiv

Article Title: Dysregulation of the p16–CDK6 axis characterizes HPV-unrelated p16-positive oropharyngeal carcinoma

doi: 10.64898/2026.08.17.743010

Figure Lengend Snippet: Normalized CDKN2A transcript counts from RNA sequencing according to HPV/p16 status in our cohort

Article Snippet: Sequencing libraries were generated with the Twist EF 2.0 Library Preparation Kit (Twist Biosciences, South San Francisco, CA, USA).

Techniques: RNA Sequencing

Journal: bioRxiv

Article Title: Dysregulation of the p16–CDK6 axis characterizes HPV-unrelated p16-positive oropharyngeal carcinoma

doi: 10.64898/2026.08.17.743010

Figure Lengend Snippet: (A) STRING network visualization of genes in the “Pathways in cancer” pathway that were commonly upregulated in HPV-unrelated OPC. (B) Schematic diagram of the p16–RB pathway. (C) CDK6 expression in RNA sequencing data stratified by HPV and CDKN2A status in the TCGA dataset. (D) Representative immunohistochemistry images of CDK6 staining. Scale bar, 200 μm. (E) IHC scores for CDK6 staining. (F) Western blot showing p16 expression in RPE1 cells with doxycycline-inducible CDK6 expression. (G) Western blot showing CDK6 expression following p16 transduction in CDKN2A-deficient FaDu cells. (H) Proportion of CDK6 expression levels in leukoplakia. CDK6 immunohistochemical staining was evaluated using a scoring system, and the distribution of scores is shown by histopathological grade. ND/LGD, non-dysplastic/low-grade dysplasia; HGD, high-grade dysplasia; SCC, squamous cell carcinoma in situ or carcinoma with minimal invasion. (I) HE and immunohistochemical images of oral leukoplakia with high-grade dysplasia showing p16 expression. Scale bars, 50 μm. (J) Clonal expansion of CDKN2A-deficient cells in CDK6-overexpressing RPE1 cells. The fraction of CDKN2A indels was quantified over time in RPE1 cells expressing the CDK6 (R31C) mutant in a doxycycline-dependent manner. DOX, doxycycline. Statistical analyses were performed using the Mann–Whitney U test in (C) and (E), and Welch’s t-test in (J). **p < 0.01, ***p < 0.001. n.s., not significant.

Article Snippet: Sequencing libraries were generated with the Twist EF 2.0 Library Preparation Kit (Twist Biosciences, South San Francisco, CA, USA).

Techniques: Expressing, RNA Sequencing, Immunohistochemistry, Staining, Western Blot, Transduction, Immunohistochemical staining, In Situ, Mutagenesis, MANN-WHITNEY

Journal: bioRxiv

Article Title: Dysregulation of the p16–CDK6 axis characterizes HPV-unrelated p16-positive oropharyngeal carcinoma

doi: 10.64898/2026.08.17.743010

Figure Lengend Snippet: (A) Schematic illustration of the CDKN2A alteration inferred from oncopanel sequencing in Case IV shown in . (B) IGV view of RNA sequencing read alignments flanking the CDKN2A deletion in the same case.

Article Snippet: Sequencing libraries were generated with the Twist EF 2.0 Library Preparation Kit (Twist Biosciences, South San Francisco, CA, USA).

Techniques: Sequencing, RNA Sequencing