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These experiments continue to provide an extraordinary volume of data describing molecular states and responses to many conditions. However, standard approaches to RNAseq analysis commonly use expression-level filters that eliminate potentially useful data in the service of decreasing noise. Here we describe the implementation of a coefficient of variation-based filter for RNAseq gene expression data. This filter prioritizes consistent data across replicates, allowing lowly expressed genes with low-variation measurements to be retained for downstream analysis. We show, using two independent Arabidopsis RNAseq datasets, that this filter allows for the inclusion of many more transcription factors than even a low-stringency expression level filter. This effect is independent of sequencing depth. We find that these lowly-expressed genes mark specific cell clusters (CCs) in our single-nucleus (sn)RNAseq dataset and may facilitate future characterization of currently unknown cell types or states. We further characterize communities of co-expressed genes, sampled across the day at two growth temperatures, in relation to snRNAseq CCs, finding evidence for a highly photosynthetic cell population and a cell state marked by high cell division and translation. These methods can be expanded to RNAseq analysis in many systems, facilitating the construction of more detailed models of tissue-specific gene regulatory networks.<\/jats:p>","DOI":"10.1093\/pcp\/pcag126","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:06:35Z","timestamp":1789473995000},"source":"Crossref","is-referenced-by-count":0,"title":["Precision-based filtering facilitates cross-referencing of conventional and single-nucleus transcriptomes to identify time- and temperature-sensitive cell populations"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9877-5474","authenticated-orcid":false,"given":"Adam","family":"Seluzicki","sequence":"first","affiliation":[{"name":"Howard Hughes Medical Institute, Salk Institute for Biological Studies , 10010 N. Torrey Pines Road, La Jolla, CA 92037 ,","place":["USA"]},{"name":"Plant Biology Laboratory, Salk Institute for Biological Studies , 10010 N. Torrey Pines Road, La Jolla, CA 92037 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8352-8956","authenticated-orcid":false,"given":"Travis A","family":"Lee","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute, Salk Institute for Biological Studies , 10010 N. Torrey Pines Road, La Jolla, CA 92037 ,","place":["USA"]},{"name":"Plant Biology Laboratory, Salk Institute for Biological Studies , 10010 N. Torrey Pines Road, La Jolla, CA 92037 ,","place":["USA"]},{"name":"Genomic Analysis Laboratory, Salk Institute for Biological Studies , 10010 N. Torrey Pines Road, La Jolla, CA 92037 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7916-7791","authenticated-orcid":false,"given":"Nolan T","family":"Hartwick","sequence":"additional","affiliation":[{"name":"Plant Biology Laboratory, Salk Institute for Biological Studies , 10010 N. Torrey Pines Road, La Jolla, CA 92037 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6272-2875","authenticated-orcid":false,"given":"Todd P","family":"Michael","sequence":"additional","affiliation":[{"name":"Plant Biology Laboratory, Salk Institute for Biological Studies , 10010 N. Torrey Pines Road, La Jolla, CA 92037 ,","place":["USA"]},{"name":"Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego , 9500 Gilman Dr., 9500 Gilman Dr., La Jolla, CA 92093 ,","place":["USA"]},{"name":"Center for Marine Biotechnology and Biomedicine, University of California San Diego , 9500 Gilman Drive, 9500 Gilman Drive, La Jolla, CA 92093 ,","place":["USA"]},{"name":"Department of Science and Conservation, San Diego Botanic Garden , 300 Quail Gardens Drive, 300 Quail Gardens Drive, Encinitas, CA 92024 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5799-5895","authenticated-orcid":false,"given":"Joseph R","family":"Ecker","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute, Salk Institute for Biological Studies , 10010 N. 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