Project description:To ascertain which genes were influenced in deletion mutants, we newly generated transcriptome data for deletion mutant vs control for each of three convergent genes (ΔNrURED, ΔNrGMF1, and ΔNrGLA) in N. rubi, respectively. After comparing the differentially expressed genes between all three mutants and controls, we found that 868 genes were identified as co-upregulated and 350 genes as co-downregulated (Figs. S7A and S7B). Gene Ontology (GO) enrichment analysis and KEGG pathway analysis revealed that these differentially expressed genes also are mainly involved in the secretory protein synthesis pathway, such as transmembrane transport, hydrolase activity, and protein processing within the endoplasmic reticulum (Figs. S7C and S7D). These results suggest that deletion of the convergent genes affected secretory protein synthesis, modification, and export.

2025-06-16 | GSE270150 | GEO

Genome assembly of silkworm BmN4 cells

Project description:BmN4 cells are cultured cells derived from Bombyx mori ovaries and widely used to study transposon silencing by PIWI-interacting RNAs (piRNAs). A high-accurate genome sequence of BmN4 cells is required to analyze the piRNA pathway using RNA-seq. The genome sequence of BmN4 cells was assembled using Pacific Biosciences (PacBio) HiFi and Oxford Nanopore technology Ultralong (ONT-UL) reads. Microscopic observation and image analysis showed that BmN4 cells were octoploid on average, and the number of chromosomes per cell was highly variable. We concluded the haplotype-resolved assembly of such a complex genome would be difficult; therefore, we assembled a consensus genome sequence. RNA-seq analysis of Siwi knockdown cells also revealed that Siwi-piRISC may target Countdown (Cd), an LTR retrotransposon. By comparing the consensus genome sequence with the reads, we identified differences between haplotypes, particulary structural variants, suggesting that some transposons, including Countdown, increased their copy number in BmN4 cells.

2025-02-03 | GSE288600 | GEO

sf21 genome assembly

Project description:SF21 cell line genome assembly

| PRJEB12116 | ENA