GEO series

Expression data from BJ-hTERT cells expressing vector, Cyclin E, c-Myc or coexpression of both

GSE28266 Homo sapiens (human) Expression microarray 7 samples Submitted 2011/03/31 Platform GPL6244

At a glance

Expression microarray · human · 7 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 7 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Chromosomal instability in early cancer stages is caused by stress on DNA replication. The molecular basis for replication perturbation in this context is currently unknown. We studied the replication dynamics in cells in which a regulator of S-phase entry and cell proliferation, the Rb-E2F pathway, is aberrantly activated. Aberrant activation of this pathway by HPV-16 E6/E7 or cyclin E oncogenes, significantly decreased the cellular nucleotide levels in the newly transformed cells.

Read the full summary ↓

Exogenously supplied nucleosides rescued the replication stress and DNA damage, and dramatically decreased oncogene-induced transformation. Increased transcription of nucleotide biosynthesis genes, mediated by expressing the transcription factor c-Myc, increased the nucleotide pool and also rescued the replication-induced DNA damage. Our results suggest a model for early oncogenesis in which uncoordinated activation of factors regulating cell proliferation leads to insufficient nucleotides that fail to support normal replication and genome stability. In order to understand the molecular basis for the low nucleotide pool in cells enforced to proliferate by oncogene expression, we performed unbiased whole transcriptome analysis of BJ cells in comparison to BJ cells expressing cyclin E, c-Myc and cells co-expressing both oncogenes. Our results suggest that Rb-E2F aberrant activation enforces cell proliferation but fails to activate the nucleotide biosynthesis pathway leading to insufficient pool of nucleotides required for normal replication.

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 (GSE28266_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 ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA139271. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21529715) ↗

Samples in this study

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+ 7 more — browse all 7 samples with per-sample file links →

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