logCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer patients (GSE80098)

This data was adopted from a study by Singhal H, et al., which was published as Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer in 2016.

data(logCPM_example)

Format

A data.frame with 7672 rows and 15 columns

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80098

Details

In this study, 12 primary malignant breast tissues (8PR+ and 4 PR-) were developed into patient-derived explants and treated with Vehicle, E2, E2+R5020, or R5020 for 24 or 48 hrs.

Raw data for 48-hr Vehicle-, R5020-treated and E2+R5020-treated samples were retrieved from GEO (GSE80098) and pre-processed into raw count. Filtration was sequentially performed to remove undetectable genes and the filtered counts were normalised using conditional quantile normalisation to offset effects of systematic artefacts, such as gene length and GC contents.

To reduce computing time, we randomly sampled half of the genes after filtration and used their logCPM value as the example data.