GEO series

Genetic variegation of clonal architecture and stem cells in leukaemia

GSE24412 Homo sapiens (human) Genome variation profiling by SNP array; SNP genotyping by SNP array 8 samples Submitted 2010/12/16 Platform GPL3718Platform GPL3720

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)

Little is known of the genetic architecture of cancer at the subclonal and single cell level or in the stem-like cells responsible for cancer clone maintenance and propagation. We have examined this issue in ALL in which ETV6-RUNX1 gene fuson is an early or initiating genetic lesion followed by a modest number of driver copy number alterations.

Read the full summary ↓

By multiplexing FISH probes for these mutations, up to eight genetic abnormalities can be detected in single cells, a genetic signature of sub-clones identified and a composite picture of sub-clonal architecture and putative ancestral trees assembled. Sub-clones in ALL have variegated genetics and complex, non-linear or branching evolutionary histories. CNA are independently and recurrently acquired in sub-clones of individual patients, and in no preferential order. Clonal architecture is dynamic and changes in the lead up to a diagnosis and in relapse. Leukaemic stem cells, assayed by transplantation in NOD/SCID IL2Rgamma deficient mice, are also genetically variegated, mirroring sub-clonal patterns. These findings have significant implications for the cancer stem cell concept, for interpretation of cancer genome data and for therapeutic targetting in cancer.

This dataset

Open GSE24412 in finder → Find more human datasets →

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 (GSE24412_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 PRJNA132711. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21160474) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

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

Datasets on a similar topic

GSE240497 Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models 66 samples shares genetic, stem
GSE277909 Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus 271 samples shares genetic, stem
GSE274546 The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X] 121 samples shares architecture, stem
GSE272080 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility [captureC] 6 samples shares architecture, genetic
GSE279619 SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation. 124 samples shares genetic
GSE339365 Genome-wide H3K4me3 profiling of circulating immune cells reveals dynamic epigenetic reprogramming during acute critical COVID-19 120 samples shares genetic
GSE299348 Single-cell epigenetic, transcriptional, protein, and TCR states of HIV-1-infected cells in gut 117 samples shares genetic
GSE282510 Multi-omics analysis in primary T cells elucidates mechanisms behind disease associated genetic loci [Hi-C] 108 samples shares genetic

Search all human datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.