GSM4680385: WT_3-wildtype-am-RNA; Mus musculus; RNA-Seq
DNA and RNA were isolated using TRIzol reagent (Sigma Aldrich, Darmstadt, Germany) and further AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) purification, following the manufacturer's instructions. For RNA isolation (RNase-free DNAse set, Qiagen) DNAse I digestion was performed on the column. Proteinase K digestion was applied for RNA and DNA isolation (Puregene Proteinase K, Qiagen). Prior to library preparation, DNA and RNA quality was checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA). All RNA samples reached an RNA integrity number (RIN) > 8.5. For the paired-end baseline as well as LPS- and medium-treated replicates of wt- and tg-AM, sequencing libraries were prepared by the DKFZ Genomics and Proteomics Core Facility from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer's instructions. For sequencing, samples were sequenced on a HiSeq 2000 v4, paired-end, 125 bp platform (Illumina). Single-end baseline replicates were prepared by the EMBL Genomics Core Facility from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.  Sequencing was performed on a Next Seq 500, single-end, 75 bp platform.
GEO Accession
GSM4680385