{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:54:24Z","timestamp":1790780064070,"version":"4.1.0"},"publisher-location":"New York, NY","reference-count":25,"publisher":"Springer US","isbn-type":[{"value":"9781071656020","type":"print"},{"value":"9781071656037","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2027]]},"DOI":"10.1007\/978-1-0716-5603-7_17","type":"book-chapter","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:55:18Z","timestamp":1790776518000},"page":"229-249","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gene Expression Analysis from Specific Root Cell Types"],"prefix":"10.1007","author":[{"given":"Alessio","family":"Terenzi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Salvi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riccardo","family":"Di Mambro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"17_CR1","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.pbi.2020.08.005","volume":"57","author":"N Svolacchia","year":"2020","unstructured":"Svolacchia N, Salvi E, Sabatini S (2020) Arabidopsis primary root growth: let it grow, can\u2019t hold it back anymore. Curr Opin Plant Biol 57:133\u2013141. https:\/\/doi.org\/10.1016\/j.pbi.2020.08.005","journal-title":"Curr Opin Plant Biol"},{"key":"17_CR2","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1093\/jxb\/err435","volume":"63","author":"T Kyndt","year":"2012","unstructured":"Kyndt T, Denil S, Haegeman A et al (2012) Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. J Exp Bot 63:2141\u20132157. https:\/\/doi.org\/10.1093\/jxb\/err435","journal-title":"J Exp Bot"},{"key":"17_CR3","unstructured":"Protocol: Basic Bulk RNA-Seq Work Flow|PGRP Roots. https:\/\/sites.lsa.umich.edu\/pgrp-roots\/protocol-basic-rna-seq-work-flow\/. Accessed 28 Dec 2025"},{"key":"17_CR4","doi-asserted-by":"publisher","first-page":"1956","DOI":"10.1126\/science.1090022","volume":"302","author":"K Birnbaum","year":"2003","unstructured":"Birnbaum K, Shasha DE, Wang JY et al (2003) A gene expression map of the Arabidopsis root. Science 302:1956\u20131960. https:\/\/doi.org\/10.1126\/science.1090022","journal-title":"Science"},{"key":"17_CR5","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1038\/nature09143","volume":"466","author":"R Sozzani","year":"2010","unstructured":"Sozzani R, Cui H, Moreno-Risueno MA et al (2010) Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 466:128\u2013132. https:\/\/doi.org\/10.1038\/nature09143","journal-title":"Nature"},{"key":"17_CR6","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1016\/j.cub.2019.02.022","volume":"29","author":"R Di Mambro","year":"2019","unstructured":"Di Mambro R, Svolacchia N, Dello Ioio R et al (2019) The lateral root cap acts as an auxin sink that controls meristem size. Curr Biol 29:1199\u20131205.e4.\u2002https:\/\/doi.org\/10.1016\/j.cub.2019.02.022","journal-title":"Curr Biol"},{"key":"17_CR7","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj2327","author":"C Ortiz-Ram\u00edrez","year":"2021","unstructured":"Ortiz-Ram\u00edrez C, Guillotin B, Xu X et al (2021) Ground tissue circuitry regulates organ complexity in maize and Setaria. Science https:\/\/doi.org\/10.1126\/science.abj2327","journal-title":"Science"},{"key":"17_CR8","doi-asserted-by":"publisher","first-page":"1362","DOI":"10.1016\/j.molp.2021.05.028","volume":"14","author":"L Serrano-Ron","year":"2021","unstructured":"Serrano-Ron L, Perez-Garcia P, Sanchez-Corrionero A et al (2021) Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation. Mol Plant 14:1362\u20131378. https:\/\/doi.org\/10.1016\/j.molp.2021.05.028","journal-title":"Mol Plant"},{"key":"17_CR9","doi-asserted-by":"crossref","unstructured":"Iyer-Pascuzzi AS, Benfey PN (2010) Fluorescence-activated cell sorting in plant developmental biology. In: Hennig L, K\u00f6hler C (eds) Plant developmental biology: methods and protocols. Humana Press, Totowa, NJ, pp 313\u2013319","DOI":"10.1007\/978-1-60761-765-5_21"},{"key":"17_CR10","unstructured":"Eurasian Arabidopsis Stock Centre (uNASC). https:\/\/arabidopsis.info\/. Accessed 28 Dec 2025"},{"key":"17_CR11","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1111\/tpj.14192","volume":"98","author":"FQ Machin","year":"2019","unstructured":"Machin FQ, Beckers M, Tian X et al (2019) Inducible reporter\/driver lines for the Arabidopsis root with intrinsic reporting of activity state. Plant J 98:153\u2013164. https:\/\/doi.org\/10.1111\/tpj.14192","journal-title":"Plant J"},{"key":"17_CR12","doi-asserted-by":"publisher","first-page":"1679","DOI":"10.1007\/s11306-015-0814-7","volume":"11","author":"SV Petersson","year":"2015","unstructured":"Petersson SV, Lind\u00e9n P, Moritz T, Ljung K (2015) Cell-type specific metabolic profiling of Arabidopsis thaliana protoplasts as a tool for plant systems biology. Metabolomics 11:1679\u20131689. https:\/\/doi.org\/10.1007\/s11306-015-0814-7","journal-title":"Metabolomics"},{"key":"17_CR13","doi-asserted-by":"publisher","first-page":"102376","DOI":"10.1016\/j.xpro.2023.102376","volume":"4","author":"A Dong","year":"2023","unstructured":"Dong A, Chan ITC, Cheung TH (2023) ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells. STAR Protoc 4:102376. https:\/\/doi.org\/10.1016\/j.xpro.2023.102376","journal-title":"STAR Protoc"},{"key":"17_CR14","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1002\/cyto.a.24792","volume":"105","author":"X Shi","year":"2024","unstructured":"Shi X, Fan W, Mehrpouyan M et al (2024) Flow cytometry analysis of protein expression using antibody-derived tags followed by CITE-Seq. Cytometry Part A 105:62\u201373. https:\/\/doi.org\/10.1002\/cyto.a.24792","journal-title":"Cytometry Part A"},{"key":"17_CR15","unstructured":"TAIR-Home. https:\/\/www.arabidopsis.org\/. Accessed 28 Dec 2025"},{"key":"17_CR16","unstructured":"Jamie Waese NP, Pasha A, Sullivan A, The BAR and other Data Analysis Tools for Plant Biology. In: https:\/\/bar.utoronto.ca\/. https:\/\/bar.utoronto.ca\/. Accessed 28 Dec 2025"},{"key":"17_CR17","unstructured":"Root Cell Atlas. https:\/\/rootcellatlas.org\/. Accessed 28 Dec 2025"},{"key":"17_CR18","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/978-1-4939-8618-7_6","volume":"1819","author":"NM Clark","year":"2018","unstructured":"Clark NM, Fisher AP, Sozzani R (2018) Identifying differentially expressed genes using fluorescence-activated cell sorting (FACS) and RNA sequencing from low input samples. Methods Mol Biol 1819:139\u2013151. https:\/\/doi.org\/10.1007\/978-1-4939-8618-7_6","journal-title":"Methods Mol Biol"},{"key":"17_CR19","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/978-1-0716-3918-4_17","volume":"2822","author":"R Hu","year":"2024","unstructured":"Hu R, Islam MN, Varghese RS, Ressom HW (2024) Short-read RNA-Seq. Methods Mol Biol 2822:245\u2013262. https:\/\/doi.org\/10.1007\/978-1-0716-3918-4_17","journal-title":"Methods Mol Biol"},{"key":"17_CR20","doi-asserted-by":"publisher","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","volume":"21","author":"A Conesa","year":"2005","unstructured":"Conesa A, G\u00f6tz S, Garc\u00eda-G\u00f3mez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674\u20133676.\u2002https:\/\/doi.org\/10.1093\/bioinformatics\/bti610","journal-title":"Bioinformatics"},{"key":"17_CR21","doi-asserted-by":"publisher","first-page":"2868","DOI":"10.1105\/tpc.19.00454","volume":"31","author":"W Decaestecker","year":"2019","unstructured":"Decaestecker W, Buono RA, Pfeiffer ML et al (2019) CRISPR-TSKO: a technique for efficient mutagenesis in specific cell types, tissues, or organs in Arabidopsis. Plant Cell 31:2868\u20132887.\u2002https:\/\/doi.org\/10.1105\/tpc.19.00454","journal-title":"Plant Cell"},{"key":"17_CR22","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1038\/s41477-020-0695-2","volume":"6","author":"X Wang","year":"2020","unstructured":"Wang X, Ye L, Lyu M et al (2020) An inducible genome editing system for plants. Nat Plants 6:766\u2013722. https:\/\/doi.org\/10.1038\/s41477-020-0695-2","journal-title":"Nat Plants"},{"key":"17_CR23","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1016\/j.tplants.2017.03.009","volume":"22","author":"T K\u00f6ster","year":"2017","unstructured":"K\u00f6ster T, Marondedze C, Meyer K, Staiger D (2017) RNA-binding proteins revisited\u2013the emerging Arabidopsis mRNA interactome. Trends Plant Sci 22:512\u2013526. https:\/\/doi.org\/10.1016\/j.tplants.2017.03.009","journal-title":"Trends Plant Sci"},{"key":"17_CR24","doi-asserted-by":"publisher","unstructured":"Zhang Z, Boonen K, Li M, Geuten K (2017) mRNA interactome capture from plant protoplasts. J Vis Exp 56011. https:\/\/doi.org\/10.3791\/56011","DOI":"10.3791\/56011"},{"key":"17_CR25","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1471-2199-7-3","volume":"7","author":"A Schroeder","year":"2006","unstructured":"Schroeder A, Mueller O, Stocker S et al (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Molecular Biol 7:3. https:\/\/doi.org\/10.1186\/1471-2199-7-3","journal-title":"BMC Molecular Biol"}],"container-title":["Methods in Molecular Biology","Root Development"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-5603-7_17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:55:19Z","timestamp":1790776519000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-5603-7_17"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"ISBN":["9781071656020","9781071656037"],"references-count":25,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-5603-7_17","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,1]]},"assertion":[{"value":"1 October 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"The authors have no conflicts of interest to declare that are relevant to the content of this chapter.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of Interest"}}]}}