Computational protocol: TIMP3 is a CLOCK-dependent diurnal gene that inhibits the expression of UVB-induced inflammatory cytokines in human keratinocytes

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Protocol publication

[…] The cells were transfected with scrambled, CLOCK, or BMAL1 siRNAs for 8 h and incubated overnight in growth medium. The cells were then synchronized with serum-rich medium for 2 h and harvested at ZT 32 and 44. Total RNAs were extracted with Trizol reagent (Thermo Fisher Scientific), and poly-A-containing mRNAs were purified and converted into a cDNA library for subsequent cluster generation and DNA sequencing, according to the instructions of the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA). Quality control checks on raw sequence data were performed by the FastQC program. For the data analysis, TopHat, Cufflinks, BWA, SamTools, Annovar, and DeFuse programs were used. […]

Pipeline specifications

Software tools FastQC, TopHat, Cufflinks, BWA, SAMtools, ANNOVAR
Application RNA-seq analysis
Organisms Homo sapiens