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Pipeline publication

[…] ologies, Santa Clara, CA). Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA) was used to remove the ribosomal RNAs. The mRNA was subsequently fragmented and used as a template for oligo (dT)-primed PCR., The cDNA libraries were prepared employing standard techniques for subsequent Illumina sequencing using the mRNA-seq Sample Prep Kit (Illumina, San Diego, CA). The cDNA libraries were sequenced on an Illumina NextSeq 500 according to the manufacturer's instructions. Sequencing raw reads were pre-processed after filtering sequencing adapters, rRNA reads, short-fragment reads, and other low-quality reads. The remaining clear reads were mapped to the reference genome of Z. bailii MT15 using Bowtie2/Tophat2 software (Langmead and Salzberg, ; Kim et al., ) based on the local alignment algorithm. Gene expression level was normalized by calculating reads per kilobase per million reads (RPKM) (Mortazavi et al., ). Differential expression of all of transcripts was quantified using DESeq software, and the method of FDR (False Discovery Rate) control was used to correct the results for multiple hypothesis testing (Anders and Huber, ). Significant DEGs were screened based on an FDR threshold of ≤0.05, and a Fold change ≥1.5. The RNA sequence data of Z. bailii MT15 at 30 and 37°C was deposited in the DNA Data Bank of Japan (DDBJ) with accession IDs DRX082892 and DRX082893, respectively., The biomass and ethanol production of Z. bailii MT15 and S. cerevisiae MT1 was determined during the fermentation process. The cell number of Z. bailii MT15 and S. cerevisiae MT1 was 9.18 × 107 and 8.18 × 107 CFU/mL at the end of fermentation (Figure ), respectively, which showed no signi […]

Pipeline specifications

Software tools Bowtie2, TopHat, DESeq
Databases DDBJ