cursons2015_se: EGF or hypoxia treatment of Breast Cancer Cell lines from...

In DavisLaboratory/emtdata: An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT)

EGF or hypoxia treatment of Breast Cancer Cell lines from Cursons et al. (2015)

Description

Dataset used in Cursons et al. 2015. where parallel ‘deep sequencing’ of RNA (RNA-Seq) were conducted to examine the changes in expression profiles between breast cancer cell lines PMC42-ET, PMC42-LA and MDA-MB-468 cells.

Format

A SummarizedExperiment object, containing gene expression data of different sub-lines of human breast cancer cell lines. The SummarizedExperiment::colData() function can be used to access the sample annotations.

Details

For PMC42 cell lines, cells were treated for 3 or 7 days in the presence or absence of 10 ng/ml EGF. For MDA-MB-468 cells, cells were treated for 7 days in the presence or absence of either 10 ng/ml EGF or kept under Hypoxia.

There are 3 biological replicates per condition which were summed. Samples were sequenced on the Illumina HiSeq 2000, 100bp paired end.

Data from this publication were downloaded from EMBL-EBI ENA and processed into a SummarizedExperiment object. Sample annotations were modified from the original publication and SRA portal.

References

Cursons, J., Leuchowius, KJ., Waltham, M., Tomaskovic-Crook, E., Foroutan, M., Bracken, CP., Redfern,A., Crampin, EJ., Street, I., Davis, MJ. & Thompson,EW. (2015) Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines. Cell Commun Signal 13, 26 (2015).

Examples

library(ExperimentHub)
eh <- ExperimentHub()
emt_datasets <- query(eh, "emtdata")

DavisLaboratory/emtdata documentation built on Nov. 24, 2024, 8:27 a.m.