GEO series

Densely interconnected transcriptional circuits control cell states in human hematopoiesis

GSE24759 Homo sapiens (human) Expression microarray 211 samples Submitted 2011/01/21 Platform GPL4685

At a glance

Expression microarray · human · 211 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 211 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Tremendous progress has been made in identifying individual transcription factors that regulate hematopoietic differentiation, but many aspects of the global architecture of hematopoiesis remain unknown. Here, we profiled gene expression in 38 distinct purified populations of human hematopoietic cells and used probabilistic models of gene expression patterns and sequence-based analysis of motifs in gene promoters to decipher the general organization of their regulatory circuitry.

Read the full summary ↓

We identified modules of highly co-expressed genes, some of which are restricted to a single lineage, but most are expressed at variable levels across multiple lineages. We found densely interconnected cis-regulatory circuits and a large number of transcription factors that are differentially expressed across hematopoietic states, suggesting a more complex regulatory system than previously assumed. We functionally validated a subset of candidate factors using RNA interference and ChIP-Seq. Our dataset, analytic tools, and findings, available on a web-based portal, provide a unique resource to study the regulatory architecture of hematopoiesis.

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 (GSE24759_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 PRJNA132159. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21241896) ↗

Samples in this study

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+ 211 more — browse all 211 samples with per-sample file links →

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