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)

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 Dec. 17, 2021, 4:09 p.m.