GSM1571344: VT_3; Mus musculus; RNA-Seq
TRAP samples underwent DNase digestion using the RNase-Free DNase Set (Qiagen, #79254) and were subsequently purified with the RNeasy MinElute Cleanup Kit (Qiagen, #74204). Eluted RNA samples were analyzed on a 2100 Bioanalyzer (Agilent) using RNA Pico Chips (Agilent, #5067-1513) to confirm RNA integrity, followed by the measurement of RNA concentrations with the Quant-iT RiboGreen RNA Assay Kit (Life Technologies, #R11490). cDNAs were prepared with the Ovation RNA-Seq System V2 kit (NuGEN, #7102-32), using an input of 1 ng RNA. 500 ng cDNA from each sample were fragmented on a Covaris S2 Focused Ultrasonicator using the operating conditions recommended by the manufacturer for a target fragment size of 200 bp. Fragment size was confirmed on a 2100 Bioanalyzer using High Sensitivity DNA Chips (Agilent, #5067-4626).Libraries for RNA sequencing were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, #RS-122-2002), starting the manufacturer’s low-throughput protocol with the end repair step. The concentration of the RNA-Seq libraries was determined on a 2100 Bioanalyzer using High Sensitivity DNA Chips. Subsequently, two libraries with different adapters were multiplexed for sequencing. After confirming the concentration of the multiplexed samples on a 2100 Bioanalyzer using High Sensitivity DNA Chips, samples were analyzed on an Illumina HiSeq 2000 sequencer using 100 bp single-end sequencing.  RNA libraries were prepared for sequencing using standard Illumina protocols
GEO
GSM1571344