Transcriptomic and proteomic data in developing tomato fruit
Tài liệu tham khảo
Biais, 2014, Remarkable reproducibility of enzyme activity profiles in tomato fruits grown under contrasting environments provides a roadmap for studies of fruit metabolism, Plant Physiol., 164, 1204, 10.1104/pp.113.231241
Belouah, 2019, Modeling protein destiny in developing fruit, Plant Physiol., 10.1104/pp.19.00086
Decros, 2019, Regulation of pyridine nucleotides metabolism along tomato fruit development through transcript and protein profiling, Front. Plant Sci., 10.3389/fpls.2019.01201
Andrews, 2010
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170
Dobin, 2015, Mapping RNA-seq reads with STAR, Curr. Protoc. Bioinforma, 11.14.1
Anders, 2015, HTSeq-A Python framework to work with high-throughput sequencing data, Bioinformatics, 31, 166, 10.1093/bioinformatics/btu638
Faurobert, 2007, Phenol extraction of proteins for proteomic studies of recalcitrant plant tissues, Methods Mol. Biol., 355, 9
Kessner, 2008, ProteoWizard: open source software for rapid proteomics tools development, Bioinformatics, 24, 2534, 10.1093/bioinformatics/btn323
Ferry-Dumazet, 2005, A web-based application to store, track, query, and compare plant proteome data, Proteomics, 5, 2069, 10.1002/pmic.200401111
Langella, 2007, The PROTICdb database for 2-DE proteomics, 279
Langella, 2013, Management and dissemination of MS proteomic data with PROTICdb: example of a quantitative comparison between methods of protein extraction, Proteomics, 13, 1457, 10.1002/pmic.201200564
Langella, 2017, X!TandemPipeline: a tool to manage sequence redundancy for protein inference and phosphosite identification, J. Proteome Res., 2, 494, 10.1021/acs.jproteome.6b00632
Valot, 2011, MassChroQ: a versatile tool for mass spectrometry quantification, Proteomics, 11, 3572, 10.1002/pmic.201100120
Belouah, 2019, Peptide filtering differently affects the performances of XIC-based quantification methods, J. Proteomics, 193, 131, 10.1016/j.jprot.2018.10.003
Wiśniewski, 2014, A “proteomic ruler” for protein copy number and concentration estimation without spike-in standards, Mol. Cell. Proteom., 13, 3497, 10.1074/mcp.M113.037309