GEO series

Affymetrix SNP array data for Genomic Instability and Myelodysplasia with Monosomy 7

GSE19523 Homo sapiens (human) Genome variation profiling by SNP array 12 samples Submitted 2010/01/13 Platform GPL2004Platform GPL2005

At a glance

human · 12 samples

Organism: Homo sapiens (human)
Topic: Myelodysplastic syndromesThis series is part of our curated briefing on it.
Samples: 12 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Gene modified autologous hematopoietic stem cells (HSC) can provide significant clinical benefits to patients suffering from X-linked chronic granulomatous disease (X-CGD), a rare inherited immunodeficiency characterized by recurrent, often life threatening bacterial and fungal infections. Here we report on the molecular and cellular events observed in two patients treated by gene therapy in 2004.

Read the full summary ↓

After the initial resolution of bacterial and fungal infections, both patients exhibited silencing of transgene expression due to methylation of the viral promoter, and myelodysplasia with monosomy 7 as a result of insertional activation of EVI1. One patient died from overwhelming sepsis 27 months after gene therapy, whereas a second patient underwent an allogeneic HSC transplantation. Our data shows that forced overexpression of MDS1/EVI1 or EVI1 in human cells disrupts normal centrosome duplication, linking MDS1/EVI1 activation to the development of genomic instability, monosomy 7 and clonal progression towards myelodysplasia.

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 (GSE19523_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 PRJNA122235. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20098431) ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

More Myelodysplastic syndromes datasets

GSE31174 Affymetrix SNP array data for myelodysplastic syndromes (MDS) and related neoplasms 58 samples same disease briefing · shares snp, affymetrix, array
GSE211032 Expression Analysis (RNA-Seq) of adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7 compared to controls 45 samples same disease briefing · shares monosomy
GSE245639 VEXAS syndrome, myelodysplasia cutis and sweet syndrome skin lesions share a common transcriptomic profile led by interferon signaling 25 samples same disease briefing · shares myelodysplasia
GSE270760 PRC2-mediated apoptosis evasion is a therapeutic target of MDS/AML harboring inv(3)/t(3;3) and monosomy 7 (CUT&Tag) 24 samples same disease briefing · shares monosomy
GSE338788 Patient Derived Neomorphic SEPTIN6 Mutations Induce Hematopoietic Stem Cell Senescence Underlying Congenital Neutropenia and Myelodysplasia 8 samples same disease briefing · shares myelodysplasia
GSE15688 Acquired mutations in TET2 are common in myelodysplastic syndromes 122 samples same disease briefing
GSE298020 PU.1-Activated Genomic Regions Define Low-risk MDS Subsets Characterized by Immune Dysregulation and Disease Progression. 493 samples same disease briefing
GSE19429 Expression data from bone marrow CD34+ cells of MDS patients and healthy controls 200 samples same disease briefing

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