Bombyx mori Transcriptome or Gene expression
Transcriptomic analysis of the silk glands of mutants (ASGs, MSGs, and PSGs) was performed for functional annotation and enrichment analysis, including gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Based on the quantitative expression results, differential gene analysis was performed between groups to obtain the genes that were differentially expressed between the two groups. The software for differential analysis was: DESeq2, and the screening thresholds were: |log2FC| >=1 &amp; padjust < 0.05. In this project, the Illumina sequencing platform was used to complete the transcriptome sequencing. In order to facilitate the analysis, distribution and sharing of sequencing data, the platform converts sequencing image signals into text signals through CASAVA Base Calling and stores them in fastq format as raw data. The fastq format is used to separate the data of each sample according to the index sequence for subsequent analysis. Each sequence in the fastq file consists of four rows of data, of which the first and third rows are read segment identifiers (the first row starts with "@" and the third with "+"), the second row is the base sequence, and the fourth row is the sequencing quality value of the bases in the second row. Illumina sequencing can generate billions of reads in a single run, and it is not possible to show the quality of each read individually; therefore, we apply statistical methods to perform statistics and quality control on the sequences measured, which can reflect the quality of library construction and sequencing quality of the samples from a macroscopic point of view. The data after quality control, i.e., clean data (reads), are compared with the reference genome to obtain mapped data (reads) for subsequent analysis, and the quality of the comparison results of this sequencing is evaluated at the same time.