Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

2013-12-26 | E-GEOD-53658 | biostudies-arrayexpress

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

Project description:Microarray was conducted on Illumina Human Ref-6 Version 2 Expression Chip (Illumina, San Diego, CA). Three independent cultures were used for RNA isolation with RNeasy plus mini kit (Qiagen, Valencia, CA). RNA quality was checked by Agilent Bioanalyzer (Agilent, Santa Clara, CA). An Ambion labeling kit was used for labeling cDNA followed by hybridization to Illumina chips. ChIP scan data was extracted by Illumina Beadstudio and subsequently analyzed using Bioconductor lumi package.

2009-04-03 | GSE15505 | GEO

miR-34a targets PDGFRA in proneural malignant glioma

Project description:To identify potential targets of miR-34a, we performed transcriptional profiling on proneural TS543 GBM cells, focusing on mRNAs whose levels decreased in response to miR-34a transfection as compared to control oligonucleotide. Proneural TS543 GBM cells were transfected with 100 nM hsa-miR-34a or control oligonucleotide using Hiperfect transfection reagent (Qiagen). After 3 days, RNA was isolated and expression analyses were performed using Illumina HT-12 bead array. The microarray dataset was normalized using a variance stable normalization (VSN) procedure in the ‘lumi’ package from the Bioconductor framework.

2012-03-26 | E-GEOD-34242 | biostudies-arrayexpress

Suppression of homeostatic T-cell proliferation by multipotent adult progenitor cells (Multistem, TM)

Project description:PCA analysis (R/Bioconductor, Lumi) revealed sample Rest202 as an outlier. This sample dataset was removed, after which data were Quantile normalized (R/Bioconductor, Lumi). Data were further analyzed in Qlucore Omics Explorer.

2015-12-31 | E-MTAB-3228 | biostudies-arrayexpress

Transcription profile of K-ras activated murine menstruating uteri

Project description:The expression of K-ras transgene is induced in K-rasV12+/-/Cre+/+/ROSA26R-LacZ+/+ transgenic mice uteri, which were primed with hormone treatment. Decidualization was artificially induced in these uteri and hormone injection was withdrawn to induced menstruation-like endometrial degeneration. Microarray was then used to study the molecular changes in these menstruating uteri following the K-ras activation. Uterine tissues were collected from K-ras induced and littermate controled menstruating uteri. Experiments were carried out using Illumina Mouse WG-6 BeadChips (n=6 in each group). Data were normalized in R environment using the Lumi Bioconductor package.

2010-06-20 | E-GEOD-15518 | biostudies-arrayexpress

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

2009-04-03 | E-GEOD-15505 | biostudies-arrayexpress

Effect of LPS on global gene expression in human skin fibroblasts

Project description:To examine responses induced by TLR4 activation at the genome-wide level, confluent fibroblasts in serum-free media were incubated with or without LPS for 6 h, and RNA was isolated using RNeasy mini kits (Qiagen, Valencia, CA). The integrity of RNA was ascertained using Agilent Bioanalyzer (Santa Clara, CA), cDNA was labeled using an Ambion labeling kit (Ambion), and hybridized to Illumina human HT-12 version 4 Expression Microarray Chips (Illumina, San Diego, CA) as described. Raw signal intensities for each probe were obtained using Illumina Beadstudio data analysis software and imported to the Bioconductor lumi package for data transformation and normalization. Probes with all samples absent (near or below background levels) were filtered. To control for multiple testing and reduce the false positive rate (FDR), stringent statistical criteria were used to identify differentially expressed genes with raw p < 0.01 and FDR adjusted p value < 0.05.

2012-03-22 | GSE36680 | GEO

TFH cell dynamics in Rhesus Monkeys during SIV infection

Project description:Cells from SIV-negative (SIVnegative_p17, n=5; SIVnegative_p18, n=5) and SIV-chronic (ChronicSIVinfection_p18, n=6) SP tissues were sorted for microarray studies. RNA samples were prepared using the Illumina beads station assay and hybridized to the Illumina HumanHT-12 version 4 Expression BeadChip according to the Illumina’s instruction. The data were normalized with the quantile normalization method of Bioconductor package limma . Missing values were imputed with R package impute (http://cran.rproject.org/web/packages/impute/index.html). Genes with significant differential expression levels were identified using Bioconductor limma package with >= 1.5 fold change (up or down), the false discovery rate (FDR) adjusted P value < 0.05.

2012-06-19 | GSE38795 | GEO

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

| 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).

2012-04-02 | E-GEOD-28475 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data