INEM Bioinformatics Hub Service Application Form

Please provide your full name to help us track your request (e.g. Lamine TOURE).

Provide a professional email address to ensure smooth communication.

Specify the team or laboratory you belong to so we can associate your request with your research group (e.g. Fabiola TERZI).

Provide a concise title for your project to quickly identify it.Example: "Lung cancer single-cell RNA-seq."

Specify whether your project is primarily exploratory (data-driven) or focused on testing a specific hypothesis (hypothesis-driven). Example: • Data-Driven: Exploring gene expression patterns in single-cell RNA-seq data. • Hypothesis-Driven: Testing whether YAP/TAZ regulate cell cycle progression in cancer cells.

Indicate the type(s) of project you're requesting support for. You can select multiple options if applicable.Example: Single-cell RNA-seq integration project.

Indicate the type of data you are working with (e.g., FASTQ, matrices, .txt files).

Provide details on the technology or platform used in your project (e.g., 10x Genomics, Smart-seq2/3, long-read/short-read sequencing, etc.).Example: 10x Genomics Chromium single-cell RNA-seq platform.

Indicate the organism(s) used in your project. You can select multiple options if applicable.Example: Human, Mouse.

Provide a brief overview of your project, including the biological question or research objective.Example:The project investigates gene expression patterns in single-cell RNA-seq data from lung cancer patients to identify potential biomarkers for early detection.

Describe the specific bioinformatics services you are requesting, such as data analysis, tool usage, or pipeline development.Example:We request assistance with data preprocessing, quality control, and differential expression analysis using Seurat and edgeR, as well as visualizations such as heatmaps and volcano plots.

Describe the experimental design, including the number of datasets and samples per dataset. Indicate the number of samples, nature of the samples (e.g., tissue, cell lines), and the experimental conditions. Example: The project includes two datasets: 1. Dataset 1: Single-cell RNA-seq from lung cancer tissue (n=5 samples from patients with and without treatment). 2. Dataset 2: Bulk RNA-seq from normal lung tissue (n=10 samples, 5 treated and 5 untreated).Experimental conditions include treatment with a specific chemotherapy drug and a control group.

Indicate the source(s) of the data used in your project. You can select multiple options if applicable.Example: Data from published results, in-house generation, etc.

Indicate the current status of the data, such as whether it is being generated, already processed, or requires further analysis.Example:Data being generated in-house, processing completed, or awaiting analysis.

Please indicate for how long the data have been available and which analysis has already been done by a platform or your team (a few sentences).Example:The data has been available for 6 months. Initial quality control was performed, followed by differential expression analysis using DESeq2, and results are ready for further functional annotation.

Indicate if any pre-analysis steps have been completed on the data (e.g., quality control, normalization, alignment). If yes, describe briefly what has been done.Example:Yes, quality control and normalization have been done using FastQC and Seurat for single-cell RNA-seq data.

Please specify which tools or software were used for the pre-analysis steps (e.g., Seurat for normalization, STAR for alignment, FastQC for quality control).Example:Quality control was done using FastQC, normalization was performed using DESeq2, and alignment was done with STAR.

What is the level of bioinformatics expertise available in your lab or research team?Example:We have a team with intermediate experience in RNA-seq analysis using DESeq2.

Please describe the bioinformatics expertise within your lab, including experience with specific analysis techniques, software proficiency, or pipeline development.Example:Our lab has advanced expertise in RNA-seq data analysis, using DESeq2 for differential expression analysis, Seurat for single-cell RNA-seq analysis, and custom pipeline development in R and Python.

Please describe why you expect the analysis to take this amount of time, considering the data complexity, analysis steps, or any specific challenges.

Do you agree to acknowledge any contribution of the Hub in authorship and to disseminate the generated code within the institute for collaborative use?Example:I agree to credit the Bioinformatics Hub for its contributions in any publications and ensure that the generated code is shared within the institute for future use.

Feel free to add any relevant comment