capture libraries  (Roche)

Journal: Science Advances

Article Title: Soma-derived 30-nt small RNAs are coupled with chromosome breakage and precisely target nontransposon DNA against elimination in Euplotes vannus

doi: 10.1126/sciadv.adx3690

Figure Lengend Snippet: ( A ) Distributions of sRNA sizes from 0 to 75 hpm. The top illustrations approximately represent the conjugating process of each sample. Colored bars represent the proportional contributions of sRNA reads. “mRNA-seq” represents the de novo–assembled transcripts that could not align with the MAC genome. ( B ) The sequence coverage of MAC chromosomes by 30-nt sRNAs (bottom) and the proportion of chromosomes producing 30-nt sRNAs (pie charts in the top panel). “All” refers to integrated sRNA reads of all samples. ( C ) The abundance correlation between 30-nt sRNA reads (normalized to transcripts per million) and genomic DNA (gDNA) reads (top) or RNA-seq reads (bottom). ( D ) Visualization of 30-nt sRNA read alignments to MAC (top) and MIC chromosomes (bottom) using Integrative Genomics Viewer (IGV). ( E ) Coverage of exons, introns, MDSs, and GSSs by 30-nt sRNAs. ( F ) Retention scores of GSSs and introns by 30-nt sRNAs. ( G ) Sequence logos of 29- to 33-nt sRNAs. ( H ) Base-wise matching frequencies of sRNAs. ( I ) Hexagonal binned plots showing sequence coverage of MAC chromosomes by sRNAs of diverse sizes. The red dashed line has a slope of 1.

Article Snippet: Before mRNA library preparation, polyadenylated RNA was isolated using magnetic beads coupling of oligo(dT) (catalog no. N401-01/02, VAHTS mRNA Capture Beads, Vazyme, China).

Techniques: Sequencing, RNA Sequencing

Journal: bioRxiv

Article Title: Riboflavin drives nucleotide biosynthesis and iron-sulfur metabolism to promote acute myeloid leukemia

doi: 10.1101/2025.06.26.661633

Figure Lengend Snippet: A . CD34 + HSPC cells nucleofected with recombinant Cas9 and sgRNAs targeting Rosa or with two independent sgRNAs targeting RFK for 15 days. Colony formation capacity was determined (left) and colony number was quantified (middle). Effective editing of RFK by the two sgRNAs was determined using Tracking of Indels by Decomposition (TIDE)-sequencing (right). B . MOLM-13 cells were treated with escalating concentrations of venetoclax and roseoflavin for 72 hours to determine viability effects. The presence of treatment synergy was determined using SynergyFinder and the Bliss synergy index and is denoted as regions of red in the graphs. The mean of three biological replicates was used for each data point. Data are presented as the mean ± SD. **** P < 0.0001 by ordinary one-way ANOVA with Bonferroni’s multiple comparisons test.

Article Snippet: Sequencing libraries (poly-A capture, non-directional library preparation) were generated by Novogene according to the manufacturer’s protocol, and were sequenced on the Illumina NovaSeq 6000, with paired end 150 bp reads (Q30 ≥ 85%) to a depth of 20 million reads per sample.

Techniques: Recombinant, Sequencing