3SRP
3SRP processes 3′ Digital Gene Expression (DGE) sequencing data to generate gene expression matrices and identify differentially expressed genes from transcriptome profiling experiments.
Key Features:
- FASTQ Demultiplexing and Transformation: Converts raw paired-end FASTQ files into single-end FASTQ files for individual samples.
- Reference Transcriptome Alignment: Aligns sequencing reads to a RefSeq reference transcriptome using BWA.
- UMI-Based Expression Quantification: Counts Unique Molecular Identifiers (UMIs) per gene in each sample to generate a gene expression matrix.
- Differential Expression Analysis: Normalizes expression matrices and identifies differentially expressed genes using DESeq2 when comparison data are provided.
- Functional Annotation: Annotates differentially expressed genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.
Scientific Applications:
- Transcriptome Profiling: Enables quantitative analysis of gene expression using 3′ Digital Gene Expression sequencing data.
- Differential Gene Expression Studies: Supports identification of condition-specific transcriptional changes across biological samples.
- Functional Genomics: Facilitates pathway and functional interpretation of differentially expressed genes using GO and KEGG annotations.
Methodology:
The workflow demultiplexes paired-end FASTQ files into single-end reads, aligns sequences to a RefSeq transcriptome using BWA, quantifies gene expression by counting Unique Molecular Identifiers (UMIs), and performs normalization and differential expression analysis with DESeq2 followed by functional annotation using GO and KEGG databases.
Topics
Details
- Maturity:
- Emerging
- Cost:
- Free of charge
- Tool Type:
- workflow
- Operating Systems:
- Linux
- Programming Languages:
- R, Python
- Added:
- 8/30/2019
- Last Updated:
- 11/24/2024
Operations
Publications
Frapin M, Guignard S, Meistermann D, Grit I, Moullé VS, Paillé V, Parnet P, Amarger V. Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus. Nutrients. 2020;12(5):1464. doi:10.3390/nu12051464. PMID:32438566. PMCID:PMC7284977.
Seiller C, Maiga S, Touzeau C, Bellanger C, Kervoëlen C, Descamps G, Maillet L, Moreau P, Pellat-Deceunynck C, Gomez-Bougie P, Amiot M. Dual targeting of BCL2 and MCL1 rescues myeloma cells resistant to BCL2 and MCL1 inhibitors associated with the formation of BAX/BAK hetero-complexes. Cell Death & Disease. 2020;11(5). doi:10.1038/s41419-020-2505-1. PMID:32371863. PMCID:PMC7200824.
Charpentier E, Cornec M, Dumont S, Meistermann D, Bordron P, David L, Redon R, Bonnaud S, Bihouée A. 3’ RNA sequencing for robust and low-cost gene expression profiling. Unknown Journal. 2021. doi:10.21203/rs.3.pex-1336/v1.
Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L, Abel L, Alcover A, Astrom K, Bousso P, Bruhns P, Cumano A, Duffy D, Demangel C, Deriano L, Di Santo J, Dromer F, Eberl G, Enninga J, Fellay J, Freitas A, Gelpi O, Gomperts-Boneca I, Hercberg S, Lantz O, Leclerc C, Mouquet H, Patin E, Pellegrini S, Pol S, Rogge L, Sakuntabhai A, Schwartz O, Schwikowski B, Shorte S, Soumelis V, Tangy F, Tartour E, Toubert A, Ungeheuer M, Quintana-Murci L, Albert ML. Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02107-w. PMID:29367672. PMCID:PMC5783949.
Bézie S, Meistermann D, Boucault L, Kilens S, Zoppi J, Autrusseau E, Donnart A, Nerrière-Daguin V, Bellier-Waast F, Charpentier E, Duteille F, David L, Anegon I, Guillonneau C. Ex Vivo Expanded Human Non-Cytotoxic CD8+CD45RClow/− Tregs Efficiently Delay Skin Graft Rejection and GVHD in Humanized Mice. Frontiers in Immunology. 2018;8. doi:10.3389/fimmu.2017.02014. PMID:29445370. PMCID:PMC5797797.
Nicol B, Salou M, Vogel I, Garcia A, Dugast E, Morille J, Kilens S, Charpentier E, Donnart A, Nedellec S, Jacq-Foucher M, Le Frère F, Wiertlewski S, Bourreille A, Brouard S, Michel L, David L, Gourraud P, Degauque N, Nicot AB, Berthelot L, Laplaud D. An intermediate level of CD161 expression defines a novel activated, inflammatory, and pathogenic subset of CD8+ T cells involved in multiple sclerosis. Journal of Autoimmunity. 2018;88:61-74. doi:10.1016/j.jaut.2017.10.005. PMID:29054368.
Picarda E, Bézie S, Boucault L, Autrusseau E, Kilens S, Meistermann D, Martinet B, Daguin V, Donnart A, Charpentier E, David L, Anegon I, Guillonneau C. Transient antibody targeting of CD45RC induces transplant tolerance and potent antigen-specific regulatory T cells. JCI Insight. 2017;2(3). doi:10.1172/jci.insight.90088. PMID:28194440. PMCID:PMC5291739.
Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-14892-x. PMID:29116112. PMCID:PMC5676863.
Pham TH, Lecomte S, Le Guevel R, Lardenois A, Evrard B, Chalmel F, Ferriere F, Balaguer P, Efstathiou T, Pakdel F. Characterization of Glyceollins as Novel Aryl Hydrocarbon Receptor Ligands and Their Role in Cell Migration. International Journal of Molecular Sciences. 2020;21(4):1368. doi:10.3390/ijms21041368. PMID:32085612. PMCID:PMC7072876.
Castel G, Meistermann D, Bretin B, Firmin J, Blin J, Loubersac S, Bruneau A, Chevolleau S, Kilens S, Chariau C, Gaignerie A, Francheteau Q, Kagawa H, Charpentier E, Flippe L, François--Campion V, Haider S, Dietrich B, Knöfler M, Arima T, Bourdon J, Rivron N, Masson D, Fournier T, Okae H, Fréour T, David L. Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells. Cell Reports. 2020;33(8):108419. doi:10.1016/j.celrep.2020.108419. PMID:33238118.