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Series GSE130373 Query DataSets for GSE130373
Status Public on Dec 27, 2019
Title Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture [Repli-Seq]
Organism Homo sapiens
Experiment type Other
Third-party reanalysis
Genome variation profiling by high throughput sequencing
Summary Human B-lineage precursor acute lymphoid leukemias (BCP-ALLs) comprise a group of genetically and clinically distinct disease entities with features of differentiation arrest at known stages of normal B-lineage differentiation. We previously showed BCP-ALL cells display unique and clonally heritable DNA-replication timing (RT) programs; i.e., programs describing the variable order of replication and sub-nuclear 3D architecture of megabase-scale chromosomal units of DNA in different cell types. To determine the extent to which BCP-ALL RT programs mirror or deviate from specific stages of normal human B-cell differentiation, we transplanted immunodeficient mice with quiescent normal human CD34+ cord blood cells and obtained RT signatures of the regenerating B-lineage populations. We then compared these with RT signatures for leukemic cells from a large cohort of BCP-ALL patients of varied genetic subtype and outcome. The results identify BCP-ALL subtype-specific features that resemble specific stages of B-cell differentiation and features that appear associated with relapse. These results suggest the genesis of BCP-ALL involves alterations in RT that reflect biologically significant and clinically relevant leukemia-specific epigenetic changes that have potential as a novel genre of prognostic biomarkers.
Overall design Genome-wide replication timing profiles were constructed from leukemia patients cells and normal differentiation stages of B-cell differentiation

Please note that the processed data 'BALLanBlood_Alldata.txt' was generated from both array and HTS data (GSE130372 and GSE130373).
Citation(s) 31698451
Submission date Apr 26, 2019
Last update date Dec 27, 2019
Contact name David M Gilbert
Organization name Florida State University
Department Biology
Lab Gilbert
Street address 319 Stadium Drive
City Tallahassee
State/province FL
ZIP/Postal code 32306-4295
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (48)
GSM3737006 AML5_10K_AML-Early S Fraction
GSM3737007 AML5_10K_AML-Late S Fraction
GSM3737008 AML5_5K_AML-Early S Fraction
This SubSeries is part of SuperSeries:
GSE130374 Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture
Reanalysis of GSM923440
Reanalysis of GSM923439
Reanalysis of GSM923450
Reanalysis of GSM923451
BioProject PRJNA539936
SRA SRP193966

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
GSE130373_BALLanBlood_Alldata.txt.gz 36.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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