RNA-Seq of rattus  norvegicus: young-adult male Kupffer cells
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany, Cat.#74104). PolyA-enriched LSEC RNA was then purified by MicroPoly(A)Purist Kit (Life Technologies, ThermoFisher Scientific, Waltham, MA), whereas Dynabeads mRNA DIRECT Micro Kit (Ambion, ThermoFisher, Cat.#61021) was used to purify mRNA from KC total RNA. The quality and quantity of mRNA quality were measured using Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, Cat.#5067-1513). The mRNAs were fragmented and reverse transcribed by Ion Total RNA-Seq Kit v2 (Life Technologies) according the manufacturers instructions. Three LSEC transcriptome libraries representing 3 biological replicates, each from one individual male Sprague Dawley rat, were constructed, whereas three KCs transcriptome libraries (=3 biological replicates) were constructed, each from the pooled KC mRNA from 2 male Sprague Dawley rats. Templates were prepared by Ion OneTouch 200 Template Kit v2 DL and Ion PGM Sequencing 300 Kit, loaded on Ion 316 chips, and sequenced with the Ion Torrent Personal Genome Machine (Life Technologies).