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Table 1 Procedures for transcriptome sequencing, data analysis and validation

From: Transcriptomic analysis of reproductive damage in the epididymis of male Kunming mice induced by chronic infection of Toxoplasma gondii PRU strain

Experimental procedureExperimental method or threshold considered
Extraction of total RNATrizol reagent (Invitrogen, CA, USA)
Quality and purity detection of total RNARNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0
cDNA library constructionThe cleaved mRNA fragments were reverse-transcribed to create the final cDNA library by the instructions of the mRNA-Seq sample preparation kit (Illumina, San Diego, USA)
Sample library constructionIllumina Hiseq 2500 sequencing platform
Transcript abundance estimationThe RPKM of each gene were calculated by the MARS model in DEGseq program, when the RPKM greater than 1000, it is considered to be a highly expressed gene
Threshold of differentially expressed genesFDR (false discovery rate) < 0.001 and |log2fold change| ≥ 1
Bioinformatics analysisGO and KEGG enrichment
Verification of mRNA expression levelReal-time fluorescence quantitative PCR
Verification of protein expression levelWestern blot