GEO series

Diversity, Topographic Differentiation, and Positional Memory in Human Fibroblasts

GSE3551 Homo sapiens (human) Expression microarray 50 samples Submitted 2005/11/03 Platform GPL3042Platform GPL1282Platform GPL3043

At a glance

Expression microarray · human · 50 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 50 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and conduit for blood and lymphatic vessels, nerves, and leukocytes. Reciprocal interactions between mesenchymal and epithelial cells are known to play a critical role in orchestrating the development and morphogenesis of tissues and organs, but the roles played by specific stromal cells in controlling the design and function of tissues remain poorly understood.

Read the full summary ↓

The principal cells of stromal tissue are called fibroblasts, a catch-all designation that belies their diversity. We characterized genome-wide patterns of gene expression in cultured fetal and adult human fibroblasts derived from skin at different anatomical sites. Fibroblasts from each site displayed distinct and characteristic transcriptional patterns, suggesting that fibroblasts at different locations in the body should be considered distinct differentiated cell types. Notablegroups of differentially expressed genes included some implicated in extracellular matrixsynthesis, lipid metabolism, and cell signaling pathways that control proliferation, cellmigration, and fate determination. Several genes implicated in genetic diseases werefound to be expressed in fibroblasts in an anatomic pattern that paralleled the phenotypicdefects. Finally, adult fibroblasts maintained key features of Hox gene expressionpatterns established during embryogenesis, suggesting that Hox genes may directtopographic differentiation and underlie the detailed positional memory in fibroblasts. Keywords: Logical Set

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 (GSE3551_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 PRJNA93623. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 12297622) ↗

Samples in this study

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+ 50 more — browse all 50 samples with per-sample file links →

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