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Transcriptome changes caused by Phf6 deletion in Committed leukemic cells from the retroviral-HoxA9 AML mouse model [RNA-seq Committed leukemic cell]

ABSTRACT: Hematopoietic conditional knockout (cKO) of Phf6 in a mouse retroviral-HoxA9 AML model led to increased transplantability. We performed bulk RNA-Seq on the 'committed' population (c-Kit+, Ly6C+) sort purified from primary recipients of HoxA9-transduced Ctrl (Vav-Cre/+, Phf6 +/Y marrow transduced with HoxA9) and cKO cells (Vav-Cre/+, Phf6 flox/Y marrow transduced with HoxA9) 8 weeks after transplantation. Our results reveal that Phf6 deletion has minimal effects on the transcriptome of the committed population (see separately deposited series for effects on the transcriptome of leukemia initiating [LIC-e] cells).

ORGANISM(S): Mus musculus

PROVIDER: GSE249109 | GEO | 2023/12/15

REPOSITORIES: GEO

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Chromatin accessibility changes caused by Phf6 deletion in Leukemia-initiating cells from the retroviral-HoxA9 AML mouse model [ATAC-Seq LICe]

Project description:Hematopoietic conditional knockout (cKO) of Phf6 in a mouse retroviral-HoxA9 AML model led to increased transplantability and accumulation of a c-Kit+ Ly6C- population that we termed the 'Leukemia Initiating Cell-Enriched' (LIC-e) population. We performed bulk ATAC-Seq on the LIC-e population sort purified 4 days after transduction of Ctrl (Vav-Cre/+, Phf6 +/Y) or cKO (Vav-Cre/+, Phf6 flox/Y) marrow retrovirally transduced with HoxA9.

2023-12-15 | GSE249110 | GEO

Microarray data from YTHDF2-deficient pre-leukemic cells and control pre-leukemic cells

Project description:YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To study the role of YTHDF2 in leukemia, c-Kit+ cells from foetal livers of Ythdf2fl/fl;Vav-iCre (Ythdf2CKO) and Ythdf2fl/fl (Ythdf2CTL) 14.5 dpc embryos were transduced with Meis1 and Hoxa9 oncogenes and serially re-plated to generate pre-leukemic cells. Total RNA from Ythdf2CKO (n=5) and Ythdf2CTL (n=5) pre-leukemic cells were used for Affymetrix global gene expression analysis.

2019-04-05 | E-MTAB-6783 | biostudies-arrayexpress

RIBO-seq analysis of YTHDF2-deficient pre-leukemic cells and control pre-leukemic cells

Project description:YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To study the role of YTHDF2 on translation regulation in leukemia, c-Kit+ cells from foetal livers of Ythdf2fl/fl; Vav-iCre (Ythdf2CKO) and Ythdf2fl/fl (Ythdf2CTL) 14.5 dpc embryos were transduced with Meis1 and Hoxa9 oncogenes and serially re-plated to generate pre-leukemic cells. RIBO-seq libraries were then prepared from Ythdf2CKO (n=3) and Ythdf2CTL (n=3) pre-leukemic cells.

2019-04-05 | E-MTAB-7785 | biostudies-arrayexpress

SLAM-Seq analysis of Ythdf2-deficient pre-leukemic cells

Project description:The mRNA m6A reader YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To study the role of YTHDF2 on mRNA decay rates in leukemia, c-Kit+ cells from foetal livers of Ythdf2fl/fl; Vav-iCre (Ythdf2CKO) and Ythdf2fl/fl (Ythdf2CTL) 14.5 dpc embryos were transduced with Meis1 and Hoxa9 oncogenes and serially re-plated to generate pre-leukemic cells. Medium with 4SU was used for pre-leukemic cells labelling for 12 hours and was later replaced with 4SU-free medium (time 0). Cells were collected immediately after medium change and at 1, 3 and 9 hours for library generation. RNA from Ythdf2CKO (n=3 biological replicates) and Ythdf2CTL (n=3 biological replicates) pre-leukemic cells were used for SLAM-seq library generation.

2019-04-05 | E-MTAB-7784 | biostudies-arrayexpress

Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (ChIP-seq)

Project description:These data include the genome wide occupancy of H2AUbq by ChIP sequencing in Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa. Immuno-precipitation of formaldehyde cross-linked chromatin prepared from Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa using H2AK119Ubq antibody.

2016-10-21 | E-GEOD-67498 | biostudies-arrayexpress

RNAseq of granulocyte-macrophage progenitors (GMP) from bone marrow of mice with hematopoietic knock-out of Rnaseh2b

Project description:Bulk transcriptomes of granulocyte-macrophage progenitor cells isolated from bone marrow of Rnaseh2bfl/fl/ Vav-Cre and Cre-negative ctrl mice; The sorted bone marrow cells had the following immunophenotype: lineage- CD201 (EPCR)- CD117+ CD16/32+ CD34+

2023-05-30 | GSE207761 | GEO

Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (RNA-seq)

Project description:These data include RNA Seq data generated from Ring1b wild type and Ring1b KO Ring1a-/- Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa. Total RNA extracted from Ring1b wild type and Ring1b KO Ring1a-/- Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa.

2016-10-21 | E-GEOD-67517 | biostudies-arrayexpress

Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (ChIP-seq)

Project description:These data include the genome wide occupancy of H2AUbq by ChIP sequencing in Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa.

2016-10-21 | GSE67498 | GEO

Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (RNA-seq)

Project description:These data include RNA Seq data generated from Ring1b wild type and Ring1b KO Ring1a-/- Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa.

2016-10-21 | GSE67517 | GEO

PBX3 cooperates with MEISI in causing rapid acute myeloid leukemia and recapitulates the core transcriptome of MLL-rearranged leukemia

Project description:To investigate whether co-expression of PBX3/MEIS1 can mimic that of MLL-AF9, HOXA9/MEIS1 or HOXA9/PBX3 in inducing leukemogenesis, we conducted in vivo mouse bone marrow transplantation (BMT) assays. Briefly, normal mouse bone marrow (BM) progenitor (i.e., lineage negative; Lin-) cells collected from B6.SJL (CD45.1) donor mice (CD45.1) were retrovirally co-transduced with MSCVneo-MLL-AF9+MSCV-PIG (MLL-AF9), MSCVneo-HOXA9+MSCV-PIG (HOXA9), MSCVneo-HOXA9+MSCV-PIG-MEIS1 (HOXA9+MEIS1), MSCVneo-HOXA9+MSCV-PIG-PBX3 (HOXA9+PBX3), MSCV-PIG-PBX3+MSCVneo-MEIS1 (PBX3+MEIS1), MSCVneo+MSCV-PIG-PBX3 (PBX3) , MSCVneo+MSCV-PIG-MEIS1 (MEIS1), or MSCVneo+MSCV-PIG (normal control; NC). Retrovirally transduced cells then were cultured with cytokines as well as puromycin and G418. Seven days later, the donor cells were transplanted into lethally irradiated (960 rads) 8- to 10-week-old C57BL/6 (CD45.2) recipient mice. The transplanted mice were watched for leukemogenesis. Then, gene expression profiling was conducted with bone marrow samples collected from leukemia groups and control group.

2016-03-03 | GSE68643 | GEO

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