sequence length  (Bioedit Company)

Journal: bioRxiv

Article Title: Programmable Repair of Disease-Causing UGA Stop Codons in Mammalian Brain

doi: 10.64898/2026.05.13.724978

Figure Lengend Snippet: (A) Premature termination codon (PTC) landscape for a variety of neurological and neurodevelopmental disorders. Prevalence varies from %13 ( SCN2A ) to 42% ( CHD2 ), with a majority caused by Arg CGA-to-TGA. (B) ClinVar submissions by stop codon type further demonstrates Arg UGA as the dominant PTC. (C) experimental layout to measure agnostic Arg UGA PTC rescue in SYNGAP1 and CDKL5 . (D) A 67-bp window centered on the mutated CGA codon (34 bp upstream and 33 bp downstream) across 19 variants from two genes: SYNGAP1 (R76, R84, R105, R485, R520, R526, R628, R716, R863, R908, R1026 and R1181) and CDKL5 (R59, R134, R550, R559, R952, R970 and R981). (E-F) positional agnostic rescue in SYNGAP1 and CDLK5 . Only one site, R134TGA in CDKL5, demonstrated poor rescue.

Article Snippet: The full-length CDKL5 sequence (RefSeq: NM_003159, Clone ID: HsCD00022404) was obtained from the DNAsu repository at The Biodesign Institute, Arizona State University.

Techniques:

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: Length distribution of transcript sequences in the full-length transcriptome of Brontispa longissima larvae.The x-axis represents the length of the transcripts. The left y-axis corresponds to the histogram, showing the number of transcripts within each length interval along the x-axis. The right y-axis represents the cumulative distribution, indicating the number of transcripts with lengths greater than or equal to a given value on the x-axis.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques:

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: Functional annotation for the full-length transcriptome of B. longissima larvae. The diagram shows the overlap of transcripts annotated against four public databases: KEGG (blue), KOG (green), Nr (orange), and Swiss-Prot (pink). The numbers in each region represent the number of transcripts annotated in the corresponding database(s), with shared regions indicating transcripts annotated in multiple databases.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques: Functional Assay

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: Nr-annotated species distribution statistics of the full-length transcriptome of (B) longissima larvae (Top 10). The X-axis represents the top 10 annotated species, while the Y-axis indicates the number of unigenes. Anoplophora glabripennis(5411 unigenes) showed the highest homology, followed by Leptinotarsa decemlineata(1858 unigenes) and Gonioctena quinquepunctata(1648 unigenes).

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques:

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: GO functional classification of the full-length transcriptome of (B) longissima larvae. The distribution of annotated unigenes is categorized into three main groups: Biological Process (red), Cellular Component (green), and Molecular Function (blue). The X-axis lists the specific Level 2 GO terms, and the Y-axis represents the number of genes associated with each term.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques: Functional Assay

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: KOG functional classification of the full-length transcriptome of (B) longissima larvae. The X-axis represents the 24 KOG categories (abbreviated from A to S), while the Y-axis indicates the number of annotated unigenes. Different colors correspond to various functional categories, with the specific class represented by each color detailed in the legend on the right. Notably, the categories “General function prediction only” (R, grey bar) and “Signal transduction mechanisms” (T, pink bar) contain the highest number of unigenes, with 2082 and 2183 respectively.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques: Functional Assay, Transduction

Journal: bioRxiv

Article Title: Role of a childhood cancer-linked BRIP1/FANCJ germline variant in genomic instability and cancer cell vulnerability

doi: 10.64898/2026.03.24.714005

Figure Lengend Snippet: a, Three-generation pedigree of an 11-year-old pediatric patient diagnosed with cancer investigated in this study. b, Whole-exome sequencing (WES) of peripheral-blood-derived DNA from the patient and both parents identified a novel missense variant in BRIP1 (c.485G>A, p.Arg162Gln) located in the nuclear localization signal (NLS), inherited from the mother, and a missense variant in HIPK2 (c.1804A>C, p.Thr602Pro), inherited from the father. c, Coomassie-stained SDS-PAGE of purified recombinant BRIP1/FANCJ WT and BRIP/FANCJ R162Q proteins. d, FAM-labeled 5’ overhang DNA substrate unwinding assay using increasing concentrations of BRIP1 WT or R162Q (1-20 nM) as indicated. Upper signal indicates the duplex substrate, the lower one the unwound FAM-labelled oligonucleotide. A representative assay is shown e, Quantification of DNA unwinding assays (n=3) shown as percentage of unwound substrate (mean ± SEM).

Article Snippet: The correct sequence of pFB-FANCJ-STREP-WT and pFB-FANCJ-R162Q-STREP constructs were verified by full length plasmid sequencing by Eurofins.

Techniques: Sequencing, Derivative Assay, Variant Assay, Staining, SDS Page, Purification, Recombinant, Labeling

Journal: bioRxiv

Article Title: Role of a childhood cancer-linked BRIP1/FANCJ germline variant in genomic instability and cancer cell vulnerability

doi: 10.64898/2026.03.24.714005

Figure Lengend Snippet: a, Schematic overview of the generation of HCT116 cell pools stably overexpressing BRIP1 WT or BRIP1 R162Q. BRIP1 WT or R162Q constructs contained C-terminal c-Myc and HA epitope tags. b, Representative Sanger sequencing traces confirming the presence of BRIP1 WT or BRIP1 R162Q in transduced HCT116 cells. c, d, Immunoblot analysis confirming expression of BRIP1 and Myc-tagged proteins in HCT116 cells expressing BRIP1 WT or R162Q, detected using BRIP1 and Myc antibodies. Vinculin served as a loading control. e, j, Functional characterization of HCT116 cells expressing BRIP1 WT or R162Q by colony formation assays following e, mitomycin C (MMC) (0.5;1; 2; 3; 4 μM/ml), g, ionizing radiation (IR) (2; 3; 4; 5 Gy), and j, hydroxyurea (HU) treatment 50;100;150;200;250 μM/ml). Representative colony plates (upper panels) and quantification of survival fractions (lower panels) are shown. Quantification was performed using EagleEye analysis software. Data represent the mean ± SD of three independent biological replicates.

Article Snippet: The correct sequence of pFB-FANCJ-STREP-WT and pFB-FANCJ-R162Q-STREP constructs were verified by full length plasmid sequencing by Eurofins.

Techniques: Stable Transfection, Construct, Sequencing, Western Blot, Expressing, Control, Functional Assay, Software