GEO series

High Density custom Agilent 44K CGH array analysis of 7q and TET2 region in myelodysplastic/myeloproliferative neoplasms

GSE21948 Homo sapiens (human) Genome variation profiling by genome tiling array 8 samples Submitted 2010/06/30 Platform GPL10452

At a glance

human · 8 samples

Organism: Homo sapiens (human)
Samples: 8 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Abnormalities of chromosome 7q are common in myeloid malignancies. Agilent CGH arrays targeted to 7q and Affymetrix SNP 6.0 arrays were used to characterise 7q aUPD and deletions. Sample #017 in this data series showed a microdeletion encompassing EZH2. Screening of a total of 614 cases with myeloid disorders revealed 49 monoallelic or biallelic EZH2 mutations in 42 individuals, most commonly myelodysplastic/myeloproliferative neoplasms (27/219; 12%) and myelofibrosis (4/30; 13%).

Read the full summary ↓

EZH2 encodes the catalytic subunit of the Polycomb repressive complex 2 (PRC2), the highly conserved histone H3 lysine 27 methyltransferase that influences stem cell renewal by epigenetic repression of genes involved in cell fate decisions. EZH2 has oncogenic activity and its overexpression has been causally linked to differentiation blocks in epithelial tumors. Unexpectedly, the mutations we identified resulted in premature chain termination or direct abrogation of histone methyltransferase activity, suggesting that EZH2 acts as a tumor suppressor for myeloid malignancies.

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 (GSE21948_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 PRJNA129387. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20601953) ↗

Samples in this study

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+ 8 more — browse all 8 samples with per-sample file links →

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GSE21990 Affymetrix SNP 6.0 array data for myelodysplastic/myeloproliferative neoplasms 148 samples shares myeloproliferative, myelodysplastic, neoplasms
GSE36823 Clonal competition with alternating dominance in multiple myeloma [44kCGH] 7 samples shares 44k, cgh
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GSE277354 Genetic charcterization of myeloproliferative neoplasms (MPN) 402 samples shares myeloproliferative, neoplasms

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