GEO series

Deep Clonal Profiling of Formalin-Fixed Paraffin-Embedded Clinical Samples

GSE40299 Homo sapiens (human) Genome variation profiling by genome tiling array 23 samples Submitted 2012/12/31 Platform GPL10123Platform GPL9777

At a glance

human · 23 samples

Organism: Homo sapiens (human)
Samples: 23 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Formalin-fixed paraffin-embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high-definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses.

Read the full summary ↓

Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues, we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas), including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE40299_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA173438. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 23226320) ↗

Samples in this study

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+ 23 more — browse all 23 samples with per-sample file links →

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