GSM1525853: Control ID FG88; Rattus norvegicus; RNA-Seq
Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007). Alpha and Beta Globin mRNA were substantially depleted from total RNA samples using the GlobinClear-Mouse/Rat Kit (Life Technologies # AM1981) as described by the vendor at EA/Quintiles; 4324 S. Alton Ave. Durham, N.C.  Analysis. Globin mRNA-depleted RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2103). Starting with 300 ng of Globin mRNA-depleted RNA, polyadenylated RNA (primarily mRNA) was selected and purified using oligo-dT conjugated magnetic beads.  Performed at EA/ Quintiles. Final cDNA libraries were analyzed for size distribution and using an Agilent 2200 TapeStation, quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824) and normalized to 2 nM for sequencing. Performed at EA/Quintiles. Clusters were generated on an Illumina cBOT using an Illumina TruSeq Paired-End Cluster Kit on an Illumina Paired End Flow Cell. The Flowcell was sequencing through 51 bases, paired end, (8 base index cycle) on an Illumina HiSeq 2000  (HiSeq Control Software v 1.5.15.1). Performed at EA/Quintiles. Quality control files contained read length and depth results (before and after clipping), presence of artifact/duplicate sequences, distribution of base quality and base frequency by sample.  Also, flow cell total yield, PF reads, barcode quality, alignment summaries and # of genes detected were determined.  FASTQ files for each RNA aliquot were generated.
GEO Accession
GSM1525853