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| Status |
Public on Oct 30, 2020 |
| Title |
Single cell characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Arrested bone marrow (BM) lymphoid cell differentiation underlies the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). Recurrent genetic lesions often directly involve transcription factors (TFs), such as ETV6 and RUNX1 found in the most common ALL translocation. Here, we studied differential gene expression in ETV6-RUNX1 primary ALL samples and the REH cell line using single cell RNA-seq (scRNA-seq).
Submitter declares that the raw data will be deposited in EGA due to patient privacy concerns.
The raw data can be accessed at https://www.ebi.ac.uk/ega/studies/EGAS00001004374
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| Overall design |
Primary patient samples from diagnosis (N=6 BM samples, subtype ETV6-RUNX1, 4000-8000 cells per donor) with day 15 post-treatment sample collected from two cases. Cell line experiment in REH comparing two drugs targeting ETS-factors (TK216 ERG/FLI1 and XRP44X ELK3) at 72 h (N=1, 900-2500 cells per treatment).
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| Contributor(s) |
Mehtonen J, Teppo S, Lahnalampi M, Kokko A, Kaukonen R, Oksa L, Laukkanen S, Bouvy-Liivrand M, Lönnberg T, Lohi O, Heinäniemi M |
| Citation(s) |
33218352 |
| Submission date |
Apr 07, 2020 |
| Last update date |
Nov 18, 2023 |
| Contact name |
Merja Heinäniemi |
| E-mail(s) |
merja.heinaniemi@uef.fi
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| Organization name |
University of Eastern Finland
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| Department |
School of Medicine
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| Street address |
Yliopistonranta 1 E
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platforms (4)
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| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
| GPL21697 |
NextSeq 550 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA623525 |
| SRA |
SRP284002 |
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