Documents

Data Files

Breast samples targeted bis-seq
The BreastSamplesTargetedBisulfiteSequencing.xlsx file contains average methylation levels over each targeted region in targeted bisulfite sequencing profiles of the 31 breast tumor and 8 normal breast samples.
07/06/2016 05:14 pm

Cell type specific amplicons
This file contains the names of the 149 amplicons from the targeted bisulfite sequencing assay used in the deconvolution of that dataset. These probes were selected due to their particularly distinct DNA methylation patterns across reference methy...
07/06/2016 05:34 pm

Cell type specific probes
This file contains the names of the 391 450k/27k probes used in the deconvolution of the TCGA dataset. These probes were selected due to their particularly distinct DNA methylation patterns across reference methylation profiles representing differ...
07/06/2016 05:35 pm

Controlled mixtures methylation
This file contains the methylation profiles of the 10 controlled cell line mixtures profiled using targeted bisulfite sequencing. These were used for initial validation of the EDec method.
07/06/2016 05:12 pm

EDec example dataset
This RData file contains a simulated data set that can be used as an example of how to use EDec.
07/12/2016 05:10 pm

Pathologist estimates H&E
This file contains the pathologist's estimates of proportions of constituent cell types for 29 breast cancer/normal samples based on H&E staining.
07/06/2016 05:17 pm

Raw targeted bisulfite sequencing methylation data
Normal Human Mammary Epithelial Cells (Clonetics), primary human fibroblasts (Asterand), human CD8+ cytotoxic T-cells (Sanguine), and breast cancer cell lines – MCF7, MDA-MB-231, MDA-MB-361, HCC1954, HCC1569, MCF10A (ATCC)—were cultured according ...
09/19/2016 02:26 pm

Reference profiles targeted bis-seq
This table contains the methylation profiles generated by targeted bisulfite sequencing of multiple cell lines. These profiles were used as references in the deconvolution of the targeted bisulfite sequencing dataset of breast tumors. They were...
07/06/2016 04:54 pm

Simulated mixtures methylation
This file contains the methylation profiles of the 100 simulated mixtures of cell types that were used in the EDec paper.
07/06/2016 05:06 pm

Simulated mixtures proportions
This file contains the true values of proportions of constituent cell types for the simulated cell type mixtures.
07/06/2016 05:08 pm

Analysis Results

Deconvoluted gene expression TCGA
This file contains the mean and standard error estimates of cell type and subtype specific gene expression profiles based on the TCGA dataset.
07/06/2016 05:42 pm

EDec estimated methylation bis-seq
This file contains the methylation profiles of constituent cell types estimated by EDec for the breast samples in targeted bisulfite sequencing dataset.
07/06/2016 05:28 pm

EDec estimated methylation TCGA
This file contains the methylation profiles of constituent cell types estimated by EDec over the set of 391 cell type specific probes based on the breast samples in the TCGA dataset.
07/06/2016 05:40 pm

EDec estimated proportions bis-seq
This file contains the proportions of constituent cell types estimated by EDec for the breast samples in targeted bisulfite sequencing dataset.
07/06/2016 05:27 pm

EDec estimated proportions TCGA
Proportions of constituent cell types estimated by EDec for the all the samples in the TCGA breast cancer dataset.
07/06/2016 05:37 pm

General

Epigenomic deconvolution (EDec) source code
This R script contains the source code for the EDec algorithm.
07/06/2016 04:46 pm

Simulate cell type mixtures
This R script contains functions that allow the user to create simulated methylation profiles of mixtures of multiple cell types, as was done in the EDec paper.
07/06/2016 04:50 pm