Journal: bioRxiv

Article Title: LASSO: versatile and selective biomolecule pulldown with combinatorial DNA-crosslinked polymers

doi: 10.1101/2025.07.24.666000

Figure Lengend Snippet: a) Percentage of RNA-seq reads mapped to rRNA for each condition. The red asterisk for the riboPOOLs data indicates the failure of one replicate to sequence properly due to the low final concentration. The bracketed red datapoint for the NEBNext condition corresponds to a sample prepared with an expired kit, which was excluded from data analysis. b) Total number of transcripts detected with >1 TPM for each condition. Statistical analysis for panels a and b was performed via an unpaired two-tailed t-test. c) All non-rRNA reads were mapped to their respective Ensembl biotype annotation, normalized to transcripts per million (TPM), and grouped by type. d) Correlation analysis of expression profiles between rRNA-depleted conditions and the undepleted condition. The six targeted rRNA transcripts are labeled. Orange data points represent outliers whose residuals lie >3 s.d. away from the linear trendline (see Methods section). Data points with black outlines indicate transcripts with high sequence similarity (>90%) to rRNA. e) Percentage of significantly affected and f) extremely affected transcripts for each method as shown in the volcano plots in Supplementary Figure 11. Transcripts with padj < 0.05 and absolute log 2 fold change > 1 or padj < 0.001 and absolute log 2 fold change > 3 are considered significantly or extremely affected, respectively. Statistical analysis was performed using a two-sided Fisher’s exact test. All data in panels a, b, and c are shown as the mean ± s.d.; data in panel d is shown as the median (n = 2 independent experiments for the riboPOOLs condition; n = 3 independent experiments for all other conditions). ns, non-significant (p > 0.05); ** p < 0.01; *** p < 0.001.

Article Snippet: Human HeLa cell total RNA (Takara Bio, catalog number 636543) was subjected to rRNA depletion with i) LASSO (Supplementary Procedure 3), ii) the riboPOOLs rRNA depletion kit with cleanUP module (siTOOLs Biotech, catalog number dp-K012-53), and iii) the fresh or expired NEBNext rRNA Depletion Kit v2 (NEB, catalog number E7400S).

Techniques: RNA Sequencing, Sequencing, Concentration Assay, Two Tailed Test, Expressing, Labeling