DMP pour le projet "Subversion immunitaire épigénétique dans les macrophages infectés par Leishmania"
Résumé
2025 3. Overview of the data 3.1. What is the purpose of the data collection/generation?
Objective 1: Mapping infection-and LSD1-dependent changes of the macrophage epigenome. ATACseq, CUT&RUN, ChemSeq and RNA seq data plus gene promoters list Objective 2: Characterization of the role of macrophage LSD1 in intracellular Leishmania infection. siRNA sequences, compounds/protacs... structures, viability assays , anti-leishmanial assays, biochemical assays Objective 3: Identification of LSD1-dependent, regulatory mechanisms required for parasite survival. Proteomic data, system level analyses, anti-leishmanial readouts 3.2. How many dataset(s) will you generate during this project? 7
3.3. What is the nature and format of generated/collected data?
Sequencing paired-end data in fastaq.gz format stored at the Biomics Institut Pasteur platform and in the NCBI public functional genomics data repository GEO (Gene Expression Omnibus) when available online for publication. Microscopy images from confocal and classical fluorescence microscopes in proprietary, tiff and PNG formats are stored in internal servers and backcopied in external hard disks
The following data are stored on hard disks and internal servers : *Real-time PCR data in .ixo format *Excel, Word, Access and PDF documents *Gel electrophoresis and WB images in jpeg, tiff and PNG formats *Liquid chromatography-tandem mass spectrometry (LC-MS/MS) data processed using myProMS v3.10.0 (https://github.com/bioinfo-pf-curie/myproms) * cytoscape data in PNG or JPEG 3.4. Give the expected volume of generated data for this project -FASTQ, a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores.
The dataset consists of Bulk RNA-Seq data derived from Mus musculus primary macrophages. The experimental design is a 2x2 factorial setup comprising: *Biological Material: Primary macrophages (uninfected vs. infected). *Treatment: Treated with an epigenetic inhibitor vs. untreated (vehicle control). *Data Type: The dataset includes raw raw sequencing reads (FASTQ format) and processed aligned data/count matrices (BAM/TXT format). 8.1.5. Describe the method of data collection and/or generation The dataset is generated and processed via the following pipeline: *Acquisition: Illumina Hiseq2500 platform; single-end 65 bp reads with strand specificity. *Pre-processing: Reads cleaned with cutadapt (v1.11); sequences <25 nt removed. *Alignment: Mapped to Reference Genome GRCm38 (Ensembl 94) using STAR (v2.5.0a). *Quantification: Gene counting via featureCounts (v1.4.6-p3) using parameters -t gene -s 0. *Availability: Publicly accessible via the NCBI Gene Expression Omnibus (GEO) repository (ongoing Superseries submission)." 8.1.6. Describe your dataset with keywords RNA-seq, Transcriptomics, Mus musculus, Primary macrophages, Epigenetics,
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