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Series GSE81730 Query DataSets for GSE81730
Status Public on Apr 03, 2019
Title Single cell gene expression profiling in normal HSCs and CML stem cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary CML stem cells (CMLSCs) and normal hematopoietic stem cells (HSCs) display the same set of surface markers (CD34+CD38-CD90+CD45RA-), making it infeasible to separate these two populations within the same sample. To overcome this challenge, and to minimize variations in gene expression due to individual variation, here we perform single-cell RNA-seq to compare expression profiles of CMLSCs and HSCs isolated from the same patient. We captured ~600 HSCs (CD34+CD38-CD90+CD45RA-) (~200 from each of three CML patient samples), separated them into CMLSCs (BCR-ABL+) or normal HSCs (BCR-ABL-) based on the presence of the BCR-ABL transcript, and performed paired-end deep sequencing. Typically, we obtained ~2.5 million mapped reads (>70% average mapping efficiency) and detected ~5,000 genes (transcript per million [TPM]>1) per cell. Despite the heterogeneity of the gene expression pattern, we were able to identify genes that were significantly more highly expressed in CMLSCs than in normal HSCs. Notably, among these genes are two cell surface markers, CD33 and CD47, that could potentially be used to distinguish CMLSCs from normal HSCs. We also found genes, such as PIM2, that could be targeted for CML therapy using available small molecule inhibitors.
Overall design Hematopoietic stem cell population from three chronic phase CML patients with no detectable BCR-ABL mutation.
Contributor(s) Ma L, Green M
Citation(s) 31068472
Submission date May 23, 2016
Last update date May 15, 2019
Contact name Michael R. Green
Organization name University of Massachusetts Medical School
Department Molecular, Cell and Cancer Biology
Lab Michael R. Green
Street address 364 Plantation Street
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (288)
GSM2174571 CML1_CMLSC1
GSM2174572 CML1_CMLSC2
GSM2174573 CML1_CMLSC3
BioProject PRJNA322448
SRA SRP075535

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Supplementary file Size Download File type/resource
GSE81730_TPMs.txt.gz 5.2 Mb (ftp)(http) TXT
GSE81730_htseq.counts.txt.gz 2.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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