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RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

ABSTRACT: RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

PROVIDER: PRJEB53833 | ENA |

REPOSITORIES: ENA

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RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR) and with or without prior TNFa treatment (IR_TNF)

Project description:Analysis of the RNA-seq data performed in IR vs NIR hematopoietic stem cells show the loss of the TNF_via_NFKB signature. We showed that the loss of this signature could be associated with hematopoietic stem cell gene deregulation. To validate this association, we tested if TNFa treatment before irradiation was able to prevent IR-effect on HSC gene deregulation. For this purpose, we treated mice with TNFa 1h before irradiation (IR_TNF) and performed RNA-seq experiments on hematopoietic stem cells 1 month after irradiation and compared them to hematopoietic stem cells sorted from non irradiated mice (NIR) and from non-treated irradiated mice (IR).

2022-06-24 | E-MTAB-11867 | biostudies-arrayexpress

H3K9me3 Cut&Tag on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR) and with or without prior TNFa treatment (IR_TNF)

Project description:Analysis of the RNA-seq data performed in IR vs NIR hematopoietic stem cells show the loss of the TNF_via_NFKB signature. We showed that the loss of this signature could be associated with H3K9me3 loss at specific retrotransposable elements . To validate this association, we tested if TNFa treatment before irradiation was able to prevent IR-effect on H3K9me3 loss at retrotransposable elements. For this purpose, we treated mice with TNFa 1h before irradiation (IR_TNF) and performed H3K9me3 cut&tag experiments on hematopoietic stem cells 1 month after irradiation and compared them to hematopoietic stem cells sorted from non irradiated mice (NIR) and from non-treated irradiated mice (IR).

2022-06-24 | E-MTAB-11864 | biostudies-arrayexpress

H3K9me3 ChIP-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

Project description:We aim at understanding how ionizing radiations (IR) increase the risk of developing myeloid leukemia. We recently showed that IR leads to the derepression of retroelements. We demonstrated that retroelements expression in aged HSCs is regulated by the heterochromatin repressive histone mark H3K9me3. However, the mechanisms by which IR specifically triggers retroelements expression in HSCs are unknown. We hypothesized that retroelements derepression is due to IR-induced heterochromatin changes. To answer this question, we performed H3K9me3 ChIP-seq experiments in hematopoietic stem cells sorted from mice one month after they were irradiated and compared them to controls hematopoietic stem cells sorted from non-irradiated mice.

2022-06-24 | E-MTAB-11865 | biostudies-arrayexpress

RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

Project description:We aim at understanding how ionizing radiations (IR) increase the risk of developing myeloid leukemia. We recently showed that IR leads to the derepression of retroelements. Retroelements are major contributors of gene regulatory networks. However, the impact of retroelements derepression on the HSC transcriptome and function remains to be addressed. We hypothesized that retroelements derepression is involved in HSC transcriptomic alterations. To answer this question, we performed RNA-seq experiments in hematopoietic stem cells sorted from mice one month after they were irradiated and compared them to controls hematopoietic stem cells sorted from non-irradiated mice.

2022-06-24 | E-MTAB-11866 | biostudies-arrayexpress

H3K9me3 ChIP-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

Project description:H3K9me3 ChIP-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

| PRJEB53831 | ENA

Project description:RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR) and with or without prior TNFa treatment (IR_TNF)

| PRJEB53832 | ENA

Project description:H3K9me3 Cut&Tag on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR) and with or without prior TNFa treatment (IR_TNF)

| PRJEB53827 | ENA

E-MTAB-11866

Project description:RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

2023-06-15 | E-MTAB-11866 | ExpressionAtlas

Determination of Nir (Noc2l) function in epidermis during mouse development by global transcriptome analysis

Project description:To investigate the role of Nir in epidermis during embryogenesis, we crossed mice harboring conditional Nir alleles with the Krt14-Cre deleter strain, which results in Cre-mediated loss of Nir selectively in epidermis. Transciptome analysis of keratinocytes obtained from control and knock-out mice at E15.5 revealed 4393 genes differentially expressed between Nir knock-out and control mice (p-value<10-2). At E17.5, we found 5673 differentially expressed genes.

2018-03-05 | GSE102277 | GEO

HUVEC T Cell Irradiation Study

Project description:Question Addresses: What is the gene expression profile from human umbilical vein endothelial cells (HUVEC) and human Jurkat T cells after irradiation (IR)? What, if any, is the effect of co-culturing these two cell types on gene expression? There are eight experimental conditions for this experiment: (1) non-irradiated HUVEC; (2) irradiated HUVEC; (3) non-irradiated Jurkat; (4) irradiated Jurkat; (5) non-irradiated HUVEC + non-irradiated Jurkat+; (6) non-irradiated HUVEC + irradiated Jurkat; (7) irradiated HUVEC + non-irradiated Jurkat; (8) irradiated HUVEC + irradiated Jurkat. A common, pooled reference consisting of RNA taken from conditions 1-8 as described above was used for all hybridizations.

2022-06-03 | GSE39019 | GEO

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