Illumina Genome Analyzer IIx paired end sequencing; GSM1172844: 184A1, RNA-Seq; Homo sapiens; RNA-Seq

184A1, RNA-Seq

56 breast cancer cell lines were profiled to identify patterns of gene expression associated with subtype and response to therapeutic compounds. Overall design: Cell lines were profiled in their baseline, unperturbed state.

Transcriptional profiling of a breast cancer cell line panel using RNAseq technology

Submitted by Gene Expression Omnibus on 11-NOV-2013

Qiagen RNAeasy RNAseq libraries for transcriptome analysis were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system per manufacturers' instructions. Sample prep began with 1 _g of total RNA from each sample. Poly-A RNA was purified from the sample with oligo dT magnetic beads, and the poly(A) RNA was fragmented with divalent cations. Fragmented poly-A RNA was converted into cDNA through reverse transcription and were repaired using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. 3' A-tailing with exo-minus Klenow polymerase was followed by ligation of Illumina paired-end oligo adapters to the cDNA fragment.  Ligated DNA was PCR amplified for 15 cycles and purified using AMPure XP beads. After purification of the PCR products with AMPure XP beads, the quality and quantity of the resulting libraries were analyzed using an Agilent Bioanalyzer High Sensitivity chip.

Transcriptional profiling of a breast cancer cell line panel using RNAseq technology

Submitter Supplied Information

Samples