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Pipeline publication

[…] rogen, Carlsbad, CA, USA) according to the manufactuerer's protocol. While RNA extaction from the filter paper culture was proceeded by firstly lyzing the cells through mortar grinding in liquid nitrogen and 5 mL TRIzolĀ® Reagent till the sample became a dried powder. The following experimental steps were the same as for cellobiose culture. NanoDrop and agarose gel electrophoresis were used to check RNA interity and concerntration (Tian et al., )., The purified RNA samples determined by Qubit 2.0 and Agilent 100 Bioanalyzer were sequenced by means of Illumina HiSeq 2500 platform to obtain the expression libraries. Prior to data analysis, the quality of raw sequencing reads was checked by the FastQC tool (v0.10.0). The clean reads were mapped against predicted transcripts from the C. ruminicola H1 genome by less than two-base mismatching, using Tophat (version 2.0.8b) (Trapnell et al., ). The normalized expression values for each gene were calculated by the number of uniquely mapped RPKM. Differential expression gene (DEG) was determined by DESeq package (v1.5.1) (Wang et al., ) with raw counts of reads mapping to unique genes as input. Genes with the transcript levels having a P < 0.01 and fold change >2 were considered as a significant differential expression, and those with fold changes of >2 or < 0.5 were defined to be up- or down-regulated genes, respectively. The transcriptome data are deposited in NCBI database under accession number of GEO ID4957774., Hierarchical clustering analysis of genes that showed significant differential expression in different experimental conditions was performed on the basis of RPKM values, using Cluster 3.0 with Euclidean distance as the similarity metric and complete linkage as […]

Pipeline specifications

Software tools FastQC, TopHat, DESeq
Chemicals Disaccharides, Glucans, Oligosaccharides