title: GSM2754343: LDLRKO Rep 3; Mus musculus; RNA-Seq
library_construction_protocol: Thioglycolate elicited peritoneal macrophages from WT and miR-33-/- mice were harvested by peritoneal lavage.  Cells were then plated for 2hr, then washed to remove non-adherant cells.  Macrophages were then scraped, pelleted and frozen at -80◦C. Total RNA from WT and miR-33-/- thioglycollate-elicited peritoneal macrophages was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNase treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). The purity and integrity of total RNA sample was verified using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries from WT BMDMs were performed TrueSeq Small RNA Library preparation (Illumina) and were sequenced for 45 cycles on Illumina HiSeq 2000 platformm (1 x 75bp read length). The reads obtained from the sequencer are trimmed for quality using in-house developed scripts.  The trimmed reads are aligned to the reference genome using TopHat2.  The transcript abundances and differences calculated using cuffdiff.  The results were plotted using R and cummeRbund using in-house developed scripts.
attributes.tag: GEO Accession
attributes.value: GSM2754343