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References from USPPAR is a cost-effective, scalable, and highly sensitive single-cell RNA sequencing workflow compatible with diverse specimens. Local targets link to admitted publications; unresolved targets remain external evidence.
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
10.1186/s13059-016-0938-8 · 2016 · External reference
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
10.1016/j.cell.2015.05.002 · 2015 · External reference
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
10.1016/j.cell.2015.04.044 · 2015 · External reference
High-throughput total RNA sequencing in single cells using VASA-seq
10.1038/s41587-022-01361-8 · 2022 · External reference
Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
10.1186/s13059-018-1407-3 · 2018 · External reference
Mapping the mouse cell atlas by microwell-seq
2018 · External reference
Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
10.1038/s41587-022-01311-4 · 2022 · External reference
Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq
10.1038/s41587-022-01312-3 · 2022 · External reference
Microfluidics-free single-cell genomics with templated emulsification
10.1038/s41587-023-01685-z · 2023 · External reference
Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding
10.1126/science.aam8999 · 2018 · External reference
The single-cell transcriptional landscape of mammalian organogenesis
10.1038/s41586-019-0969-x · 2019 · External reference
A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains
10.1038/s41588-023-01572-y · 2023 · External reference
A panoramic view of cell population dynamics in mammalian aging
10.1126/science.adn3949 · 2025 · External reference
Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium
10.1186/s12915-017-0359-5 · 2017 · External reference
An improved procedure for utilizing terminal transferase to add homopolymers to the 3′ termini of DNA
10.1093/nar/9.16.4173 · 1981 · External reference
Stability of endogenous and added RNA in blood specimens, serum, and plasma
10.1093/clinchem/48.10.1647 · 2002 · External reference
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
10.1038/s41591-020-0844-1 · 2020 · External reference
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
10.1186/s13059-020-02048-6 · 2020 · External reference
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
10.1038/s41587-020-0465-8 · 2020 · External reference
The tabula sapiens: a multiple-organ, single-cell transcriptomic atlas of humans
2022 · External reference
Sex differences orchestrated by androgens at single-cell resolution
10.1038/s41586-024-07291-6 · 2024 · External reference
Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
10.1101/gr.253880.119 · 2019 · External reference
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
10.1186/s13059-019-1906-x · 2019 · External reference
Single-cell transcriptional profiling of splenic fibroblasts reveals subset-specific innate immune signatures in homeostasis and during viral infection
10.1038/s42003-021-02882-9 · 2021 · External reference
Single-nucleus and in situ RNA-sequencing reveal cell topographies in the human pancreas
10.1053/j.gastro.2020.11.010 · 2021 · External reference
Single-cell RNA sequencing reveals the landscape of maize root tips and assists in identification of cell type-specific nitrate-response genes
10.1016/j.cj.2022.02.004 · 2022 · External reference
A cis-regulatory atlas in maize at single-cell resolution
10.1016/j.cell.2021.04.014 · 2021 · External reference
Deep generative modeling for single-cell transcriptomics
10.1038/s41592-018-0229-2 · 2018 · External reference
Transgelin is a TGFβ-inducible gene that regulates osteoblastic and adipogenic differentiation of human skeletal stem cells through actin cytoskeleston organization
10.1038/cddis.2016.196 · 2016 · External reference
clustifyr: an R package for automated single-cell RNA sequencing cluster classification
10.12688/f1000research.22969.2 · 2020 · External reference
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
10.1101/gr.177881.114 · 2014 · External reference
Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants
10.1093/protein/gzs034 · 2012 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Cell fixation and preservation for droplet-based single-cell transcriptomics
10.1186/s12915-017-0383-5 · 2017 · External reference
Glyoxal as an alternative fixative for single-cell RNA sequencing
10.1093/g3journal/jkad160 · 2023 · External reference
A standardized nomenclature for mammalian histone genes
10.1186/s13072-022-00467-2 · 2022 · External reference
10.1101/2022.08.27.505512
10.1101/2022.08.27.505512 · 2022 · External reference
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
10.1038/s41587-020-0469-4 · 2020 · External reference
Comprehensive single-cell transcriptional profiling of a multicellular organism
10.1126/science.aam8940 · 2017 · External reference
RNA velocity—current challenges and future perspectives
2021 · External reference
Bayesian approach to single-cell differential expression analysis
10.1038/nmeth.2967 · 2014 · External reference
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies
2025 · External reference
Acyl fluorides: fast, efficient, and versatile lysine-based protein conjugation via plug-and-play strategy
10.1021/acs.bioconjchem.7b00141 · 2017 · External reference
Proteomics. Tissue-based map of the human proteome
10.1126/science.1260419 · 2015 · External reference
Ribonuclease A mutant His119 Asn: the role of histidine in catalysis
10.1016/s0014-5793(96)01173-8 · 1996 · External reference
Unresolved reference
2009 · External reference
Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes
10.1016/j.jprot.2020.103793 · 2020 · External reference
Optimized single-nucleus transcriptional profiling by combinatorial indexing
10.1038/s41596-022-00752-0 · 2022 · External reference
Purification of proteins using polyhistidine affinity tags
10.1016/s0076-6879(00)26058-8 · 2000 · External reference
Metal chelate affinity chromatography, a new approach to protein fractionation
10.1038/258598a0 · 1975 · External reference
Covalent labeling with diethylpyrocarbonate: sensitive to the residue microenvironment, providing improved analysis of protein higher order structure by mass spectrometry
10.1021/acs.analchem.9b01732 · 2019 · External reference
RNA structure determination using chemical methods
10.1101/pdb.prot078485 · 2013 · External reference
Integrating Single-cell RNA-seq to construct a Neutrophil prognostic model for predicting immune responses in non-small cell lung cancer
10.1186/s12967-022-03723-x · 2022 · External reference
Mapping the developing human immune system across organs
2022 · External reference
Protocol: optimised methodology for isolation of nuclei from leaves of species in the Solanaceae and Rosaceae families
10.1186/1746-4811-9-31 · 2013 · External reference
Systematic methods for isolating high purity nuclei from ten important plants for omics interrogation
10.3390/cells11233919 · 2022 · External reference
Comparison of four nuclear isolation buffers for plant DNA flow cytometry
10.1093/aob/mcl141 · 2006 · External reference
Calcium at the cell wall-cytoplast interface
10.1111/j.1744-7909.2010.00923.x · 2010 · External reference
scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases
2024 · External reference
Microarray detection method for pathogen genes by on-chip signal amplification using terminal deoxynucleotidyl transferase
2022 · External reference
Applications of terminal deoxynucleotidyl transferase enzyme in biotechnology
10.1002/cbic.202200510 · 2023 · External reference
The active site and mechanism of action of bovine pancreatic ribonuclease
10.1038/190781a0 · 1961 · External reference
Copper binding to the prion protein: structural implications of four identical cooperative binding sites
10.1073/pnas.96.5.2042 · 1999 · External reference
Nucleases
10.1016/b978-012243740-3/50006-5 · 1996 · External reference
Enzymatic and chemical-based methods to inactivate endogenous blood ribonucleases for nucleic acid diagnostics
10.1016/j.jmoldx.2020.04.211 · 2020 · External reference
Polyvinylsulfonic acid: a low-cost RNase inhibitor for enhanced RNA preservation and cell-free protein translation
10.1080/21655979.2017.1313648 · 2017 · External reference
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
10.1186/s13059-018-1603-1 · 2018 · External reference
High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq
10.1038/s41467-023-38409-5 · 2023 · External reference
Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets
10.1186/s13073-021-00941-8 · 2021 · External reference
Microbial single-cell RNA sequencing by split-pool barcoding
10.1126/science.aba5257 · 2021 · External reference
Multiplexed intact-tissue transcriptional analysis at cellular resolution
10.1016/j.cell.2016.01.038 · 2016 · External reference
Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
10.7554/elife.73971 · 2022 · External reference
Simple cDNA normalization using kamchatka crab duplex-specific nuclease
10.1093/nar/gnh031 · 2004 · External reference
Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution
10.1126/science.aaw1219 · 2019 · External reference
The OP9-DL1 system: generation of T-lymphocytes from embryonic or hematopoietic stem cells in vitro
10.1101/pdb.prot5156 · 2009 · External reference
Unresolved reference
2015 · External reference
Protein production by auto-induction in high density shaking cultures
10.1016/j.pep.2005.01.016 · 2005 · External reference
Chemically defined conditions for human iPSC derivation and culture
10.1038/nmeth.1593 · 2011 · External reference
STAR: ultrafast universal RNA-seq aligner
10.1093/bioinformatics/bts635 · 2013 · External reference
SCANPY: large-scale single-cell gene expression data analysis
10.1186/s13059-017-1382-0 · 2018 · External reference
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
10.1186/s13059-014-0550-8 · 2014 · External reference
Unresolved reference
External reference
10.1007/978-3-319-24277-4
10.1007/978-3-319-24277-4 · 2016 · External reference
Unresolved reference
External reference
Data visualization using R for researchers who do not use R
2022 · External reference
Unresolved reference
External reference
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
10.1371/journal.pone.0163962 · 2016 · External reference
Cutadapt removes adapter sequences from high-throughput sequencing reads
10.14806/ej.17.1.200 · 2011 · External reference
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data
10.1093/bioinformatics/btaa1009 · 2021 · External reference
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
10.1016/j.xinn.2021.100141 · 2021 · External reference
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data
2023 · External reference
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
10.1016/j.cell.2021.12.018 · 2022 · External reference
Unresolved reference
External reference
Glyoxal as an alternative fixative to formaldehyde in immunostaining and super-resolution microscopy
10.15252/embj.201695709 · 2018 · External reference
Gene expression profiling of non-polyadenylated RNA-seq across species
10.1016/j.gdata.2014.07.005 · 2014 · External reference
