RNA-seq analysis of shCTR and shSF3B1 NHD13-derived HSPC (cKIT+) cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA815341 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18305207.fastq.gz | Fastqsanger.gz | |||
| SRR18305208.fastq.gz | Fastqsanger.gz | |||
| SRR18305209.fastq.gz | Fastqsanger.gz | |||
| SRR18305210.fastq.gz | Fastqsanger.gz | |||
| SRR18305211.fastq.gz | Fastqsanger.gz |
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2023-03-21 | GSE198464 | GEO
Project description:Investigation of differences in gene expression between NHD13 mice with myelodysplastic syndrome and wild type littermates. RNA was harvested from Lineage negative Kit positive cells purified from mice transgenic for NHD13 or wild type littermates. Samples were pooled in groups of 3. 3 replicates were performed for each genotype.
2012-07-26 | E-GEOD-39692 | biostudies-arrayexpress
Project description:Recurring deletions of chromosome 7 and 7q [-7/del(7q)] occur in myelodysplastic syndromes and acute myeloid leukemia (AML) and are associated with poor prognosis. However, the identity of specific tumor suppressors on 7q remains elusive. Using RNAi and CRISPR/Cas9 approaches, we show that a ~50% reduction in gene dosage of the mixed lineage leukemia 3 (MLL3) gene, located on 7q36.1, cooperates with other events occurring in -7/del(7q) AMLs to promote leukemogenesis. Mll3 suppression impairs the differentiation of HSPC. Interestingly, Mll3 suppressed leukemias, like human -7/del(7q) AMLs, are refractory to conventional chemotherapy but sensitive to the BET inhibitor JQ1. Thus, our mouse model functionally validates MLL3 as a haploinsufficient 7q tumor suppressor, and suggests a therapeutic option for this aggressive disease. Total RNA obtained from sorted lin-ckit+ hematopoietic stem and progenitor cells of recipient mice transplanted with shRen;p53-/- or shMll3;p53-/- cells at 6 weeks after transplant
2014-03-19 | E-GEOD-54313 | biostudies-arrayexpress
Project description:Investigation of differences in gene expression between NHD13 mice with myelodysplastic syndrome and wild type littermates.
2012-07-27 | GSE39692 | GEO
Project description:T-cell Acute Lymphoblastic Leukaemia (T-ALL) can be classified into a number of subfamilies, including those that overexpress TAL1/LMO, TLX1/3 and HOXA transcription factors. Whilst it has been previously shown in mouse models that TAL1/LMO transcription factors induce thymocyte self-renewal, whether this is the case for other transcription factor subclasses is currently unknown. To address this, we have studied vav-Nup98-HoxD13-transgenic (NHD13-Tg) mice, a model of HOXA-driven T-ALL, which overexpress HOXA transcription factors throughout haematopoiesis and display features of myelodysplastic syndrome in the bone marrow along with T-cell developmental abnormalities in the thymus and subsequent development of T-ALL in approximately 15% of mice. Thymocytes from preleukemic NHD13-Tg mice could engraft long-term in serial transplantation assays, demonstrating that NHD13-Tg thymocytes have acquired self-renewal capacity. Transcriptome analysis showed that NHD13-Tg thymocytes exhibited a Stem Cell like transcriptional program which closely resembled that of Lmo2 transgenic thymocytes, including Lmo2 itself and the critical Lmo2 cofactor Lyl1, suggesting a common mechanism of thymocyte self-renewal in these models. To determine whether Lmo2/Lyl1 are required for NHD13-induced thymocyte self-renewal, NHD13-Tg mice were crossed with Lyl1 knockout mice to generate NHD13-Tg mice lacking Lyl1. This showed that Lyl1 is essential for expression of the stem cell-like gene expression program in NHD13-Tg thymocytes and for thymocyte self-renewal. Surprisingly however, absence of Lyl1 accelerated the onset of T-ALL in NHD13-Tg mice. These studies demonstrate that Lyl1 is essential for self-renewal of NHD13-Tg thymocytes, suggesting that Lmo2 and Lyl1 may mediate thymocyte self-renewal induced by a variety of T-cell oncogenes. However, whilst Lyl1-induced thymocyte self-renewal is essential for Lmo2-driven T-cell leukemia, NHD13 can also promote T-ALL via an alternative pathway.
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2016-07-03 | E-GEOD-66264 | biostudies-arrayexpress
Project description:Analysis of Lin-c-Kit+Sca-1- haematopoietic stem cells (HSCs) expressing the Nup98-HoxD13 (NHD13) fusion gene. NHD13 induces myelodysplastic syndrome (MDS) in mice. Results provide insight into the molecular basis of the myelodysplastic phenotype
2016-01-01 | GSE66264 | GEO
Project description:Whole exome sequencing (the SureSelectXT Mouse All Exon Kit) was done on leukemias from NP23-NHD13 double transgenic mice with strain background designated “C57Bl6-NIH”.
2020-09-10 | GSE137542 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. To determine the molecular mechanism of severe cytopenia in NHD13+ Tg mice, we purified Lin-Sca-1+c-Kit+CD34-Flt3-CD150+ HSCs from WT and NHD13+Tg mice at 4 month of age and perform the RNA-seq analysis. Methods: Trizol was used to extract RNA from FACS sorted CD150+CD34–Flt3–LSK viable cells. Total RNA was used for quality controls and for normalization of starting material. cDNA-libraries were generated with 10 ng of total RNA using the SMARTer Ultra Low RNA Kit for Illumina Sequencing according to the manufacturer’s indications. Sequencing was done using the Illumina Next-Gen Sequencing HiSeq platform with 30-45 million 75bp, paired-end reads. Results: We found 597 genes with significantly differential expression in NHD13+ HSCs, compared to WT controls (p<0.001). The expression of NUP98-HOXD13 up-regulated the expression of HOX genes, including Hoxa3, Hoxa5, Hoxa7, Hoxa9, Hoxb6, Hoxc5, Hoxc6, Hoxc8, Hoxc9 and Hoxd3, the important myeloid transcription factor Pbx3, cell cycle regulators, Cdk6 and Cdc25C, as well as the transcripts encoding the Ly6d surface membrane protein. We then performed pathway analyses, which showed that DNA duplication, DNA damage response and cell cycle-related genes, were more highly expressed in NHD13+ HSCs than WT HSCs, while multiple metabolic process-related gene pathways were downregulated. Conclusions: Our analyses demonstrate that the gene expression signature defined in murine NHD13+ MDS HSCs displays robust similarities with the gene expression profiles of human MDS cells, strongly suggesting that this murine MDS model can be used to accurately model human MDS.
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