GEO series

Expression data from bone marrow CD34+ cells of MDS patients and healthy controls

GSE19429 Homo sapiens (human) Expression microarray 200 samples Submitted 2010/03/13 Platform GPL570

At a glance

Expression microarray · human · 200 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Myelodysplastic syndromesThis series is part of our curated briefing on it.
Samples: 200 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

In order to gain insight into the molecular pathogenesis of the myelodysplastic syndromes (MDS), we performed global gene expression profiling and pathway analysis on the hematopoietic stem cells (HSC) of 183 MDS patients as compared with the HSC of 17 healthy controls. The most significantly deregulated pathways in MDS include interferon signaling, thrombopoietin signaling and the Wnt pathway.

Read the full summary ↓

Among the most significantly deregulated gene pathways in early MDS are immunodeficiency, apoptosis and chemokine signaling, whereas advanced MDS is characterized by deregulation of DNA damage response and checkpoint pathways. We have identified distinct gene expression profiles and deregulated gene pathways in patients with del(5q), trisomy 8 or –7/del(7q). Patients with trisomy 8 are characterized by deregulation of pathways involved in the immune response, patients with –7/del(7q) by pathways involved in cell survival, whilst patients with del(5q) show deregulation of integrin signaling and cell cycle regulation pathways. This is the first study to determine deregulated gene pathways and ontology groups in the HSC of a large group of MDS patients. The deregulated pathways identified are likely to be critical to the MDS HSC phenotype and give new insights into the molecular pathogenesis of this disorder thereby providing new targets for therapeutic intervention.

This dataset

Open GSE19429 in finder → Find more human microarray datasets → Myelodysplastic syndromes landscape →

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 (GSE19429_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 PRJNA122295. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20220779) ↗

Samples in this study

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+ 200 more — browse all 200 samples with per-sample file links →

More Myelodysplastic syndromes datasets

GSE284647 The genotype-integrated gene expression profile at the single-cell level of bone marrow CD34-positive hematopoietic stem and progenitor cells (HSPCs) from a patient with myelodysplastic neoplasms (MDS) harboring germline and somatic DDX41 variants. 1 samples same disease briefing · shares cd34, mds, marrow, bone
GSE326589 Bone marrow immunosuppressive states associate with survival after guadecitabine and atezolizumab therapy in HMA-R/R MDS 58 samples same disease briefing · shares mds, marrow, bone
GSE316079 SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome [ATAC-seq] 6 samples same disease briefing · shares mds, marrow, bone
GSE316081 SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome [RNA-seq] 6 samples same disease briefing · shares mds, marrow, bone
GSE288862 ScRNA-Seq of Human MDS and AML Bone Marrow Marrow Microenvironment. 3 samples same disease briefing · shares mds, marrow, bone
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 mds, controls
GSE280881 Rapid Disease Progression of Myelodysplastic Syndrome is Reflected in Transcriptomic and Functional Abnormalities of Bone Marrow MSCs 22 samples same disease briefing · shares marrow, bone
GSE279914 Molecular fingerprints for bone marrow cells, myelodysplastic syndrome and aplastic anemia 14 samples same disease briefing · shares marrow, bone

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