HC_1; HC_2; HC_3
Total RNA was isolated with PAXgeneBlood RNA Kit using the standard protocol. To minimize the biological variation among population, within each group (SLE patient and HC), equal amounts of sample from 8 different individuals were randomly pooled. For each group, three biological replicate samples of patient (SLE_1; SLE_2; SLE_3) and control (HC_1; HC_2; HC_3), were included. The final total RNA was dissolved in 200 l RNase-free water (New England BioLabs) to remove residual DNA. The concentration of total RNA was determined by NanoDrop (Thermo Scientific), and the RNA integrity value (RIN) was checked using RNA 6000 Pico LabChip of Agilent 2100 Bioanalyzer (Agilent).  The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina). The poly(A) containing mRNA molecules were purified using Sera-mag Magnetic Oligo(dT) Beads (Illumina) from 20 mg total RNA of each sample. Ten milli molar Tris-HCl was used to elute the mRNA from the magnetic beads. To avoid priming bias when synthesizing cDNA, the mRNA was first fragmented before cDNA synthesis. The mRNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved mRNA fragments were converted to double-stranded cDNA using SuperScript II, RNaseH and DNA Pol I, primed by random primers. The resulting cDNA was purified using the QIA quick PCR Puriﬁcation Kit (Qiagen). Then, cDNA was subjected to end-repair and phosphorylation using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, and subsequent purification was performed using QIA quick PCR Puriﬁcation Kit (Qiagen). These repaired cDNA fragments were 30-adenylated using KlenowExo (Illumina) and purifiedusing MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single ‘A’ base overhung at their 30-ends for subsequent adapter-ligation. Illumina PE adapters were ligated to the ends of these 30-adenylated cDNA fragments, followed by purification using MinElute PCR Purification Kit. To select a size range of templates for downstream enrichment, the products of the ligation reaction were purified on a 2% TAE-agarose gel (Certified Low-Range Ultra Agarose, Biorad). A range of cDNA fragments (200 ± 25 bp) was excised from the gel and extracted using QIA quickGel Extraction Kit (Qiagen). Fifteen rounds of PCR amplification were performed to enrich the adapter modified cDNA library using primers complementary to the ends of the adapters [PCR Primer PE 1.0 and PCR Primer PE 2.0 (Illumina)]. The PCR products of size 200 ± 25 bp were purified using QIAquick GelExtraction Kit except that Qiaquick spincolumns were substituted with MinElute spin columns (Qiagen). Finally, after quantification on an Agilent Technologies 2100 Bioanalyzer using the Agilent DNA1000 chip kit, the cDNA library products were sequenced using the Illumina HiSeq 2000 according to manufacturers’ protocols.  Raw reads were filtered using a fastx tool kit and then mapped to the human genome (hg19).