GSM3067400: A2-Tmem-Stim; Mus musculus; RNA-Seq
We had 24 samples stored frozen in TRIzol until RNA extraction (young (Y) and aged (A); replicate 1 and replicate 2, with cells pooled from 4 mice in each replicate; TN, TVM and TMEM cells; unstim and stim match across each replicate). Due to lane capacity limits for sequencing, we processed these samples for RNA and sequencing in two batches (Batch 1- Y1_Tn_Unstim, Y1_Tvm_Unstim, Y1_Tmem_Unstim, Y1_Tn_Stim, Y1_Tvm_Stim, Y1_Tmem_Stim, A1_Tn_Stim, A1_Tvm_Stim, A1_Tmem_Stim, A2_Tn_Stim, A2_Tvm_Stim, A2_Tmem_Stim. Batch 2- Y2_Tn_Unstim, Y2_Tvm_Unstim, Y2_Tmem_Unstim, Y2_Tn_Stim, Y2_Tvm_Stim, Y2_Tmem_Stim, A1_Tn_Unstim, A1_Tvm_Unstim, A1_Tmem_Unstim, A2_Tn_Unstim, A2_Tvm_Unstim, A2_Tmem_Unstim). Of note, in Batch 2 we ran a duplicate of Y1_Tn_Unstim (Y1_Tn_Unstim_norm) to test for any batch effect, but none was observed. RNA was extracted using chloroform extraction followed by isopropanol precipitation, extracted RNA was treated with recombinant DNAse I (Roche) according to the manufacturer's instructions then purified using the RNeasy MinElute Cleanup columns (Qiagen) and analysed for RNA quality using the RNA 6000 Nano kit (Agilent) on an Agilent 2100 Bioanalyzer. Samples were prepared with the Illumina TruSeq RNA v2 sample preparation protocol (cDNA synthesis, adapter ligation, PCR amplification) (Illumina) and run using 100 bp paired end sequencing on an Illumina Hi-Seq. Samples were prepared with the Illumina TruSeq RNA v2 sample preparation protocol (cDNA synthesis, adapter ligation, PCR amplification) (Illumina) and run using 100 bp paired end sequencing on an Illumina Hi-Seq.