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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 procedure Experimental method or threshold considered
Extraction of total RNA Trizol reagent (Invitrogen, CA, USA)
Quality and purity detection of total RNA RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0
cDNA library construction The 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 construction Illumina Hiseq 2500 sequencing platform
Transcript abundance estimation The 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 genes FDR (false discovery rate) < 0.001 and |log2fold change| ≥ 1
Bioinformatics analysis GO and KEGG enrichment
Verification of mRNA expression level Real-time fluorescence quantitative PCR
Verification of protein expression level Western blot