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ShRNA kinome screen identifies TBK1 as therapeutic target for HER2+ breast cancer

ABSTRACT: Microarray analysis was performed at the UHN Microarray Centre (UHNMAC, Ontario, Canada) using Illumina HumanHT-12 v4 BeadChip with 500 ng of total RNA prepared by RNeasy mini kit (QIAGEN, Cat. No. 74104). Samples from HCC1954 cells with 3-day treatment of TBK1-II at 4 uM were used to compare with vehicle-treated controls. Microarray data was processed and normalized by lumi package from BioConductor in R with Quantile Method. Difference between the samples were calculated by Bayesian statistic using limma package from BioConductor in R to obtain Moderated T value for subsequent Pathway analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53658 | GEO | 2013/12/26

SECONDARY ACCESSION(S): PRJNA232595

REPOSITORIES: GEO

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shRNA kinome screen identifies TBK1 as therapeutic target for HER2+ breast cancer

Project description:Microarray analysis was performed at the UHN Microarray Centre (UHNMAC, Ontario, Canada) using Illumina HumanHT-12 v4 BeadChip with 500 ng of total RNA prepared by RNeasy mini kit (QIAGEN, Cat. No. 74104). Samples from HCC1954 cells with 3-day treatment of TBK1-II at 4 uM were used to compare with vehicle-treated controls. Microarray data was processed and normalized by lumi package from BioConductor in R with Quantile Method. Difference between the samples were calculated by Bayesian statistic using limma package from BioConductor in R to obtain Moderated T value for subsequent Pathway analysis. Total RNA extracted from HER2+ HCC1954 cells after 3 days treatment of TBK1-II inhibitor compared with vehicle control

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Expression of cyclophilin B is associated with malignant progression and regulation of genes

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shRNA kinome screen identifies TBK1 as therapeutic target for HER2+ breast cancer

Project description: Not available

| S-ECPF-GEOD-53658 | biostudies-other

Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples

Project description:Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases. Investigation of data preprocessing techniques for DASL-assayed RNA samples from frozen brain tissue. IVT- and DASL-based expression assays were performed on 10 reference RNA samples (brain and pooled artificially degraded at 0, 10, 30, and 60 min), 4 formalin-fixed tissue-extracted RNA samples with replicates, and 57 frozen tissue-extracted RNA samples with replicates. A subset of the 57 (N=33 samples) from frozen brain tissue assayed using the DASL-based platform were then used to test different dataset preprocessing strategies implemented in the lumi package in R/Bioconductor. The data from frozen-tissue extracted DASL-processed RNA samples passing exclusion criteria were log2 transformed and normalized using quantile normalisation with lumi in R (quantile-normalized data available as a supplementary file linked to the Series record).

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