Computational protocol: TGF-β3 Inhibits Antibody Production by Human B Cells

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Protocol publication

[…] RNA was extracted using RNeasy Micro Kit (Qiagen), and libraries were prepared using TruSeq Stranded mRNA LT Kit (Illumina). Paired-end sequencing was performed using HiSeq 2500 (Illumina). Cutadapt[] and FASTX-Toolkit ( were used to remove adaptor sequences and ends with phred quality scores less than 20. UCSC hg19 reference sequence ( was used as the reference genome, and STAR[] was used for mapping. Read count was obtained for each gene using HTSeq[]. Read count after quality control was 4.9x106 ~ 9.7x106. Differential gene analysis was performed using edgeR 3.12.0[]. Pathway analysis was performed by uploading genes with false discovery rate less than 0.05 by the Benjamini-Hochberg method and their logFCs into IPA software (Qiagen)[]. R version 3.2.3 was used for RNA-Seq analysis. […]

Pipeline specifications

Software tools cutadapt, FASTX-Toolkit, STAR, HTSeq, edgeR
Application RNA-seq analysis
Organisms Homo sapiens, Mus musculus
Diseases Autoimmune Diseases, Lupus Erythematosus, Systemic