Olaparib Resistance RNA Sequencing

RNA was isolated from PEO1 olaparib-sensitive (n = 2) and four PEO1 olaparib-resistant clones using RNeasy columns with on-column DNase digest (Qiagen). RNA quality was confirmed using an Agilent Tapestation and all RNA used for library preparation had a RIN > 9. Libraries were created using Illumina TruSEQ stranded mRNA library prep (#RS-122-2102). Strand-specific pair-ended libraries were pooled and run on HiSeq4000 (Illumina). Library creation and sequencing were performed at the University of Colorado Genomics Core. HISAT [37 (link)] was used for alignment against GRCh37 version of the human genome. Samples were normalized using transcripts per kilobase million (TPM) measurement and gene expression using the GRCh37 gene annotation was calculated using home-made scripts. Analysis was performed by the Division of Translational Bioinformatics and Cancer Systems Biology at the University of Colorado School of Medicine. Data have been deposited to NCBI GSE117765.

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Watson Z.L., Yamamoto T.M., McMellen A., Kim H., Hughes C.J., Wheeler L.J., Post M.D., Behbakht K, & Bitler B.G. (2019). Histone methyltransferases EHMT1 and EHMT2 (GLP/G9A) maintain PARP inhibitor resistance in high-grade serous ovarian carcinoma. Clinical Epigenetics, 11, 165.

Publication 2019

on-column DNase digest Tapestation TruSEQ stranded mRNA library prep HiSeq4000

Cancer Clones Dnase Gene annotation Gene expression Human genome Library Medicine Mrna Olaparib Translational

Corresponding Organization :

Other organizations : University of Colorado Denver, University of Colorado Anschutz Medical Campus, University of Colorado Cancer Center

Top 5 similar protocols

Variable analysis

independent variables

Olaparib-sensitivity

dependent variables

Gene expression

control variables

RNA quality (RIN > 9)
RNA isolation method (RNeasy columns with on-column DNase digest)
Library preparation method (Illumina TruSeQ stranded mRNA library prep)
Sequencing platform (HiSeq4000)
Alignment method (HISAT against GRCh37 human genome)
Normalization method (TPM)

controls

Positive control: Not specified
Negative control: Not specified

Annotations

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