Journal: PeerJ

Article Title: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro

doi: 10.7717/peerj.4017

Figure Lengend Snippet: Heatmap representing the most abundant genera (at least 0.1% on average) showed no clear effect of treatment with 5-FU on the gut microbial composition as determined by 16S rRNA gene amplicon sequencing.

Article Snippet: 16S rRNA gene amplicon sequencing was performed by LGC Genomics (Berlin, Germany) on the Illumina MiSeq platform.

Techniques: Amplification, Sequencing

Journal: PeerJ

Article Title: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro

doi: 10.7717/peerj.4017

Figure Lengend Snippet: NMDS plots based on Bray Curtis dissimilarities of 16S rRNA gene amplicon sequencing data at day 6 (after treatment) showed large interindividual variability (5-FU: p = 0.0001, R 2 = 70.1%; SN-38: p = 0.0001, R 2 = 44.3%), but no clear effect of the treatment with (A) 5-FU ( p = 0.75, R 2 = 2.7%) or (B) SN-38 ( p = 0.31, R 2 = 5.1%).

Article Snippet: 16S rRNA gene amplicon sequencing was performed by LGC Genomics (Berlin, Germany) on the Illumina MiSeq platform.

Techniques: Amplification, Sequencing

Journal: PeerJ

Article Title: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro

doi: 10.7717/peerj.4017

Figure Lengend Snippet: Confouding factors explaining variation in microbial community composition. P -values and R for different confounding factors based on Bray-Curtis dissimilarities of the 16S rRNA gene Illumina amplicon sequencing data (significant values are indicated in italic).

Article Snippet: 16S rRNA gene amplicon sequencing was performed by LGC Genomics (Berlin, Germany) on the Illumina MiSeq platform.

Techniques: Amplification, Sequencing

Journal: PeerJ

Article Title: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro

doi: 10.7717/peerj.4017

Figure Lengend Snippet: Heatmap representing the most abundant genera (at least 0.1% on average) showed no clear effect of treatment with SN-38 on the gut microbial composition as determined by 16S rRNA gene amplicon sequencing.

Article Snippet: 16S rRNA gene amplicon sequencing was performed by LGC Genomics (Berlin, Germany) on the Illumina MiSeq platform.

Techniques: Amplification, Sequencing

Journal: bioRxiv

Article Title: Validated CRISPR/Cas9 guide RNAs targeting neurodevelopmental genes in the tunicate Ciona robusta

doi: 10.64898/2026.03.25.711585

Figure Lengend Snippet: Selected sgRNA target sites are indicated, along with Amplicon-EZ (Genewiz) indel plots and estimated mutagenesis rates. Red arrows indicate CRISPR-generated indel peaks. Grey asterisks indicate naturally-occurring indels. Mutagenesis rates are approximated for plots in which naturally occurring indels confounded automatic rate estimation.

Article Snippet: In all, 25 sgRNAs targeting the 8 genes were tested by a standard, commercially available Illumina-based, next-generation target site amplicon sequencing service (Amplicon-EZ by Genewiz) as previously described ( ).

Techniques: Amplification, Mutagenesis, CRISPR, Generated

Journal: bioRxiv

Article Title: Validated CRISPR/Cas9 guide RNAs targeting neurodevelopmental genes in the tunicate Ciona robusta

doi: 10.64898/2026.03.25.711585

Figure Lengend Snippet: Selected sgRNA target sites are indicated, along with Amplicon-EZ (Genewiz) indel plots and estimated mutagenesis rates. Red arrows indicate CRISPR-generated indel peaks. Grey asterisks indicate naturally-occurring indels. Mutagenesis rates are approximated for plots in which naturally occurring indels confounded automatic rate estimation.

Article Snippet: In all, 25 sgRNAs targeting the 8 genes were tested by a standard, commercially available Illumina-based, next-generation target site amplicon sequencing service (Amplicon-EZ by Genewiz) as previously described ( ).

Techniques: Amplification, Mutagenesis, CRISPR, Generated

Journal: bioRxiv

Article Title: Validated CRISPR/Cas9 guide RNAs targeting neurodevelopmental genes in the tunicate Ciona robusta

doi: 10.64898/2026.03.25.711585

Figure Lengend Snippet: All sgRNA target sequences tested in this study, along with predicted efficacy scores from CRISPOR, namely Doench ‘16 and Doench Ruleset 3 (RS3). Norm. ‘16 and Norm. RS3 represents normalized Doench ‘16 and Doench RS3 scores, in which the represented ranges (not absolute theoretical score ranges) are converted to a scale from 0 to 1. Norm+Ave = normalized Doench ‘16 and RS3 scores averaged. Mut. % = mutagenesis efficacy as measured by Amplicon-EZ sequencing. Mut. % scores in blue represent efficacies estimated from size of indel peak, and not the automated efficacies as given by automated Amplicon-EZ analysis (black Mut. % scores).

Article Snippet: In all, 25 sgRNAs targeting the 8 genes were tested by a standard, commercially available Illumina-based, next-generation target site amplicon sequencing service (Amplicon-EZ by Genewiz) as previously described ( ).

Techniques: Mutagenesis, Amplification, Sequencing

Journal: bioRxiv

Article Title: Validated CRISPR/Cas9 guide RNAs targeting neurodevelopmental genes in the tunicate Ciona robusta

doi: 10.64898/2026.03.25.711585

Figure Lengend Snippet: A) Selected Tyrosinase sgRNA target sites are indicated, along with Amplicon-EZ (Genewiz) indel plots and estimated mutagenesis rates. Mutagenesis rates are approximated for plots in which naturally occurring indels confounded automatic rate estimation. B) Left: diagram of simple pigmentation assay (see text for details). Right: results of pigmentation assay of Tyr CRISPR larvae using sgRNAs 1.185 and 5.16 together (40 µg each) in combination with 50 µg Sox1/2/3>Cas9::Geminin Nterminus . ( ; ). CRISPR larvae (n = 45) were compared to negative control larvae (n = 29) electroporated with 80 µg of the “control” sgRNA plasmid instead . Plasmid DNA amounts indicated per 700 µl of total electroporation volume. Statistical significance determined using Fisher’s exact test. C) Selected VAChT sgRNA target sites indicated, along with indel plots. Dashed red line indicates alternative splicing of first exon with remaining exons encoding choline acetyltransferase (ChAT) out of view, as part of a conserved cholinergic locus. Red arrows indicate CRISPR-generated indel peaks. Grey asterisks indicate naturally-occurring indels.

Article Snippet: In all, 25 sgRNAs targeting the 8 genes were tested by a standard, commercially available Illumina-based, next-generation target site amplicon sequencing service (Amplicon-EZ by Genewiz) as previously described ( ).

Techniques: Amplification, Mutagenesis, CRISPR, Negative Control, Control, Plasmid Preparation, Electroporation, Alternative Splicing, Generated

Journal: bioRxiv

Article Title: Validated CRISPR/Cas9 guide RNAs targeting neurodevelopmental genes in the tunicate Ciona robusta

doi: 10.64898/2026.03.25.711585

Figure Lengend Snippet: Plots comparing predicted efficacy scores (Doench ‘16, Doench Ruleset 3/RS3, or normalized/averaged Doench scores) to actual mutagenesis efficacies as measured/estimated by Amplicon-EZ sequencing. All data according to the table in . Pearson’s correlations calculated and shown for each set of predictions.

Article Snippet: In all, 25 sgRNAs targeting the 8 genes were tested by a standard, commercially available Illumina-based, next-generation target site amplicon sequencing service (Amplicon-EZ by Genewiz) as previously described ( ).

Techniques: Mutagenesis, Amplification, Sequencing