NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE111085 Query DataSets for GSE111085
Status Public on Apr 09, 2018
Title Distinct Transcriptomic and Exomic Abnormalities within Myelodysplastic Syndrome Marrow Cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Prior studies using DNA microarray platforms have shown alterations of gene expression profiles (GEPs) of marrow cells in myelodysplastic syndromes (MDS). Using the increased sensitivity and accuracy of high-throughput RNA sequencing (RNA-Seq) for detecting and quantifying mRNA transcripts, our study has demonstrated novel significant differences in GEPs between MDS and normal CD34+ marrow cells with 41 genes identified as disease classifiers. Additionally, two main clusters of GEPs distinguished patients based on their major clinical features, particularly between those whose disease remained stable (sMDS) vs patients whose illness transformed to acute myeloid leukemia within 12 months (tMDS). The genes whose expression was associated with disease outcome were involved in functional pathways and biologic processes highly relevant for MDS. Exomic analysis identified MDS-associated pathogenic mutations in virtually all patients tested. MDS subgroups with spliceosome mutations demonstrated distinct differential isoform usage and expression and consequent dysregulation of distinct biological functions. This combination of clinical, transcriptomic and exomic findings provides valuable molecular insights into the mechanisms underlying MDS and its progression to a more aggressive stage and also facilitates prognostic characterization of MDS patients.
 
Overall design RNA-Seq was performed on CD34+ hematopoietic stem cells derived from healthy individuals and patients with myelodysplastic syndrome.
 
Contributor(s) Rao V, Greenberg P
Citation(s) 29616851
Submission date Feb 25, 2018
Last update date Mar 27, 2019
Contact name Varsha Rao
E-mail(s) varshar@stanford.edu
Phone 6507245777
Organization name Stanford University
Department Genetics
Lab Snyder Lab
Street address 300 Pasteur Drive
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (67)
GSM3021862 MDS1281_tMDS_RNA-seq
GSM3021863 MDS1251_tMDS_RNA-seq
GSM3021864 MDS1112_sMDS_RNA-seq
Relations
BioProject PRJNA435879
SRA SRP133442

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE111085_MDS_genes_edgeR.txt.gz 7.4 Mb (ftp)(http) TXT
GSE111085_MDS_isoform_fpkm.txt.gz 7.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap