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A long noncoding RNA expression atlas of normal and malignant hematopoiesis

Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression, epigenetics and cell fate decisions. To better define their roles in hematopoiesis, we profiled miRNA, lncRNA and mRNA expression in purified human hematopoietic stem cells (HSCs) and their differentiated progeny, including granulocytes, monocytes, T-cells, NK cells, B-cells, megakaryocytes and erythroid cells. We further compared these ncRNA landscapes with those of 46 pediatric AML patient samples. For each blood cell population, over 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs were quantified on 146 arrays.

T-distributed stochastic neighbor embedding (t-SNE) on lncRNAs and miRNAs robustly structured our dataset into groups matching the input cell populations, underlining the cell type-specific expression patterns of ncRNA genes. Self-organizing maps (SOMs) further identified clusters of coordinately upregulated genes in hematopoietic stem cells and pediatric AMLs. Through the lncScape online app, the expression levels of manifold miRNAs and lncRNAs can be retrieved across normal and malignant hematopoiesis. Since our resource includes fingerprint lncRNAs for every cell type, gene set enrichment analyses, plus class prediction of co-expressed coding genes, users can infer functions for every transcript.
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A catalog of advanced lentiviral CRISPR-Cas9 delivery vectors from our laboratory

The recent discovery and application of the CRISPR-Cas9 system has enabled unprecedented versatility and simplicity in genome editing. CRISPR-Cas9-based technologies are now used to inactivate genes, correct genetic mutations, induce large genomic deletions and chromosomal translocations, and even to control transcription and epigenetics. Our lab has developed a range of modular Cas9, sgRNA, and all-in one plasmids for efficient delivery of the CRISPR-Cas9 system into murine and human hematopoietic cells. We leverage these to model translocation-driven leukemiogenesis, to delineate the sequential acquisition of mutations during leukemia progression, to perform targeted gene correction, and to inhibit or activate the expression of non-coding RNAs. The sgRNA constructs can be used singly or multiplexed for large-scale forward-genetic screens.

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