ice inference of crispr edits software  (Synthego Inc)

Journal: bioRxiv

Article Title: CRISPR/Cas12a-Mediated Knockout of the INNER NO OUTER ( INO ) Gene in Musa balbisiana cv. Bhimkol

doi: 10.64898/2026.05.13.724745

Figure Lengend Snippet: A) Induction of embryonic calli from male flowers of Bhimkol after 6 months of culture. B) A magnified view at 40x of embryogenic calli. C) Establishment of ECS after 8 months of culture was used for genetic transformation mediated through Agrobacterium harboring pSS03. D) Embryonic calli in selection medium with 40 mg/L hygromycin, and 250 mg/L timentin. E) A magnified view of putative transformed mature somatic embryos at 40x magnification. F) Shoots regeneration in M4 medium containing 40 mg/L hygromycin, and 250 mg/L timentin after one month of culture. G) Rooting from i n vitro regenerated shoots in the R1 rooting medium containing 40 mg/L hygromycin, and 250 mg/L timentin after 14 days of culture. H) Putative CRISPR-edited Bhimkol plantlets with healthy shoots and roots, ready for hardening.

Article Snippet: Furthermore, analysis using ICE (Inference of CRISPR Edits) software from Synthego showed that lines 03_06 and 03_17 harboured 4-bp deletions within the target region at positions 97–100 and 96–99, respectively.

Techniques: Transformation Assay, Selection, CRISPR

Journal: bioRxiv

Article Title: CRISPR/Cas12a-Mediated Knockout of the INNER NO OUTER ( INO ) Gene in Musa balbisiana cv. Bhimkol

doi: 10.64898/2026.05.13.724745

Figure Lengend Snippet: CRISPR-edited Bhimkol plants transferred to the transgenic net house, A) 03_01, B) 03_05, C) 03_06, D) 03_17 and E) Wild Type (Control)

Article Snippet: Furthermore, analysis using ICE (Inference of CRISPR Edits) software from Synthego showed that lines 03_06 and 03_17 harboured 4-bp deletions within the target region at positions 97–100 and 96–99, respectively.

Techniques: CRISPR, Transgenic Assay, Control

Journal: bioRxiv

Article Title: CRISPR/Cas12a-Mediated Knockout of the INNER NO OUTER ( INO ) Gene in Musa balbisiana cv. Bhimkol

doi: 10.64898/2026.05.13.724745

Figure Lengend Snippet: Sequence analysis of the INO gene in CRISPR/Cas12a-edited lines. Amino acid sequences from lines 03_01, 03_05, 03_06, and 03_17 were aligned with the wild type sequence. Red asterisks indicate stop codons.

Article Snippet: Furthermore, analysis using ICE (Inference of CRISPR Edits) software from Synthego showed that lines 03_06 and 03_17 harboured 4-bp deletions within the target region at positions 97–100 and 96–99, respectively.

Techniques: Sequencing, CRISPR

Journal: bioRxiv

Article Title: CRISPR/Cas12a-Mediated Knockout of the INNER NO OUTER ( INO ) Gene in Musa balbisiana cv. Bhimkol

doi: 10.64898/2026.05.13.724745

Figure Lengend Snippet: Analysis of YABBY and HMG-box_2 domain in the WT and CRISPR-edited lines. The CRISPR-edited Bhimkol lines exhibit a complete absence of the HMG_box_2 and truncated YABBY domains.

Article Snippet: Furthermore, analysis using ICE (Inference of CRISPR Edits) software from Synthego showed that lines 03_06 and 03_17 harboured 4-bp deletions within the target region at positions 97–100 and 96–99, respectively.

Techniques: CRISPR

Journal: Neuro-Oncology

Article Title: Autophagy modulates glioblastoma cell sensitivity to Selinexor-mediated XPO1 inhibition

doi: 10.1093/neuonc/noae280

Figure Lengend Snippet: Enhanced autophagic flux is an on-target effect of Selinexor in glioblastoma cells. ( A ) DNA sequence read from GBM43 cells ( bottom ) and GBM43 cells in which a CRISPR knock-in approach ( top ) encoding C528S mutant (mut) XPO1. ( B ) The visualization ( top ) and lowest bind energy ( bottom ) of molecular docking between Selinexor (Slx) and XPO1 wildtype/mut protein. ( C ) Representative immunofluorescence analysis ( top ) and quantitation ( bottom ) of GBM43 and GBM43mut cells incubated for 24 h with 0 or 1000 nM Selinexor, then analyzed for RanBP1 co-localization with nuclear DAPI staining (10–15 cells/group). ( D ) ( Left ) cell viability (normalized to control cells) of GBM43 and GBM43mut cell lines following 72 h continuous incubation with varying concentrations of Selinexor, and ( right ) IC50 values of Selinexor for GBM43 and GBM43mut cell lines. ( E ) Representative photos of clonogenic assays performed using GBM43 and GBM43mut cells continuously exposed to 0, 100, 200, or 400 nM Selinexor for 14 days. ( F ) Representative Western blot analysis of LC3B-I, LC3B-II, and ACTIN levels in GBM43 and GBM43mut cells lines incubated with DMSO, Selinexor (750 nM, 72 h) or rapamycin (500 nM, 16 h), or with non-targeted siRNA or a pool of siRNA targeting XPO1 (48 h after a 24-h siRNA incubation). ( G ) Viable number of GBM43 and GBM43mut cells (normalized to control cells) monitored daily after incubation with non-targeted siRNA or a pool of siRNA targeting XPO1 as in (F). Except where noted, all quantitated values listed are the means of 3 experiments. CYS, Cysteine; SER, Serine. ***, P ≤ .001.

Article Snippet: Complete replacement of wildtype (WT) XPO1 with C528S mutant (mut) XPO1 was confirmed using Synthego’s Inference of CRISPR Edits (ICE) software tool (Synthego Performance Analysis, ICE Analysis, v3.0).

Techniques: Sequencing, CRISPR, Knock-In, Mutagenesis, Immunofluorescence, Quantitation Assay, Incubation, Staining, Control, Western Blot

Journal: bioRxiv

Article Title: CRISPR screening reveals SYCP3 as a key driver of metastasis in prostate cancer

doi: 10.1101/2025.01.30.629925

Figure Lengend Snippet: A The Inference of CRISPR Edits (ICE) software output of the analyses of the Sanger sequencing data on the SYCP3 gene part flanking the exon 1 of the ORF. B Invasion analysis in DU145 cells using 10% FBS as a chemoattractant. Top panels, representative images of cells (bars: 100 µm); bottom panels, histograms showing the mean value ± S.E.M. of the percentage of invasive cells (n = 3). C Migration analysis of DU145 cells using a wound healing assay (n=3). D-F Adhesion/spreading analysis of DU145 cells. Representative images of adhered DU145 cells (C) and histograms showing the mean value ± S.E.M. of the percentage of adhered cells (D) or areas covered (E) of SYCP3 depleted cells referred to NTC cells (n = 3). Scale bars: 100 μm. G Immuno-fluorescence microscopy images of phalloidin staining ( red ) adhered NTC and SYCP3 depleted DU145 cells. Cell nuclei were stained with DAPI ( blue ). Scale bars: 100 μm. H-I Histograms showing the cytoskeleton (G) or nuclei area value ± S.E.M. of adhered DU145 indicated cells (n=2). Statistic tests: Student t test ( B, C ), two-way ANOVA ( E, F ) and U-Mann Whitney test ( H, I) . *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

Article Snippet: DNA sequencing chromatograms were analyzed using the Inference of CRISPR Edits (ICE) free software tool (synthego.com/products/bioinformatics/crispranalysis).

Techniques: CRISPR, Software, Sequencing, Migration, Wound Healing Assay, Fluorescence, Microscopy, Staining, MANN-WHITNEY