Madrak1984/RNAseq_code_Evi1_TPO: RNAseq pipeline analysis for the Evi1 TPO experiments
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2025
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| _version_ | 1866902189738295296 |
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| author | Seguin, Jonathan |
| author_facet | Seguin, Jonathan |
| contents | <p>This page contains code used for the bioinformatics analysis of RNAseq dataset to study the impact of Evi1 (part of Mecom gene) expression and exogenous TPO on iKMT2A-MLLT3 transgenic mice on the appearance of Acute Myeloid Leukemia.<br><br>Hematopoietic Stem-cells were filtered from bone marrow tissues after exposure of TPO treatment. Cells were grouped according to the expression of Evi1 genes (marked by GFP) in 3 different groups, Evi1+, Evi1- and bulk. <br><br>To compare the results with human datasets, bioinformatic analysis of RNAseq datas from TARGET, BEAT, Leucegene and St-Jude hospital was analyzed according to the gene-fusion presence (KMT2A-MLLT3, KMT2A-rearrangement or Evi1 groups). Clustering of patients data were done according to the intern expression of MECOM and ERG genes. Differential expression analyses was performed according the clusters of interest.<br><br>All theses analysis are used for the paper "Thrompoietin increases susceptibility for EVI1+ KMT2A-MLLT3-driven AML expressing stel cell genes linked to poor outcome. The code for each analysis and figures creation is stored in the Src folder. The folder Snakemake contains the rds files with the reads count per gene from the Ensembl version 102 of mouse genome from the RNAseq of transgenic mices. The folder Dataset contains human datasets used from TARGET, BEAT, Leucegene and St-Jude hospital publicly available on their respective website and GEO. <span lang="EN-GB"><br><br><br>For more information, please contact seguin.jonathan@gmail.com<br></span></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_16845288 |
| institution | Zenodo |
| language | eng |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Madrak1984/RNAseq_code_Evi1_TPO: RNAseq pipeline analysis for the Evi1 TPO experiments Seguin, Jonathan <p>This page contains code used for the bioinformatics analysis of RNAseq dataset to study the impact of Evi1 (part of Mecom gene) expression and exogenous TPO on iKMT2A-MLLT3 transgenic mice on the appearance of Acute Myeloid Leukemia.<br><br>Hematopoietic Stem-cells were filtered from bone marrow tissues after exposure of TPO treatment. Cells were grouped according to the expression of Evi1 genes (marked by GFP) in 3 different groups, Evi1+, Evi1- and bulk. <br><br>To compare the results with human datasets, bioinformatic analysis of RNAseq datas from TARGET, BEAT, Leucegene and St-Jude hospital was analyzed according to the gene-fusion presence (KMT2A-MLLT3, KMT2A-rearrangement or Evi1 groups). Clustering of patients data were done according to the intern expression of MECOM and ERG genes. Differential expression analyses was performed according the clusters of interest.<br><br>All theses analysis are used for the paper "Thrompoietin increases susceptibility for EVI1+ KMT2A-MLLT3-driven AML expressing stel cell genes linked to poor outcome. The code for each analysis and figures creation is stored in the Src folder. The folder Snakemake contains the rds files with the reads count per gene from the Ensembl version 102 of mouse genome from the RNAseq of transgenic mices. The folder Dataset contains human datasets used from TARGET, BEAT, Leucegene and St-Jude hospital publicly available on their respective website and GEO. <span lang="EN-GB"><br><br><br>For more information, please contact seguin.jonathan@gmail.com<br></span></p> |
| title | Madrak1984/RNAseq_code_Evi1_TPO: RNAseq pipeline analysis for the Evi1 TPO experiments |
| url | https://doi.org/10.5281/zenodo.16845288 |