GEO series

Fine mapping of androgen regulated genes in LNCaP cells

GSE18684 Homo sapiens (human) Expression microarray 96 samples Submitted 2010/09/01 Platform GPL6102

At a glance

Expression microarray · human · 96 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 96 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Detailed analysis of androgen regulated gene expression in the LNCaP prostate cancer cell line. Since androgens and the AR are known to be important for prostate cancer cell proliferation and invasion we aimed to identify androgen receptor (AR) regulated genes by combining this detailed Illumina beadarray study of androgen regulated gene expression with AR ChIP-sequencing data.

Read the full summary ↓

LNCaP cells were grown in RPMI medium supplemented with 10% charcoal dextran stripped (steroid depleted) FBS for 72h, before treatment with 1nM R1881 or vehicle control. Total RNA was harvested every 30min for 4h and then every hour up to 24h using trizol (Sigma), quantified using a Nanodrop spectrophotometer (ND-1000). RNA samples were prepared for analysis on Illumina Human 6 v2 BeadArrays and Biotrove Realtime PCR panels according to the manufacturers protocols (see Supplementary Methods for details). Expression array data were normalised in R using the beadarray software and BASH (see Supplementary Methods for details) (Cairns et al., 2008; Dunning et al., 2007).

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 (GSE18684_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 PRJNA121563. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21602788) ↗

Samples in this study

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+ 96 more — browse all 96 samples with per-sample file links →

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