biostudies-literatureHe WGeneral Program of National Natural Science Foundation of ChinaNatural science foundation of Science and Technology Commission of Shanghai MunicipalityNational Natural Science Foundation of ChinaNational Key Research and Development Program of China384https://www.ebi.ac.uk/biostudies/studies/S-EPMC12606830biostudies-literatureUnknown26(1)High-throughput sequencing with chemical labeling enables robust, transcriptome-wide detection of RNA modifications at single-nucleotide resolution. However, these methods typically require substantial RNA amounts due to harsh treatments. We introduce Uli-epic, an innovative library construction strategy that enables profiling epitranscriptomic modifications using 100 pg to 1 ng of RNA. Utilizing Uli-epic BID-seq, we investigate pseudouridine (Ψ) sites in neural stem cells and sperm RNA from wild-type and fetal growth restriction mice, using only 500 pg of rRNA-depleted RNA. Uli-epic GLORI quantifies m⁶A in sperm and neural stem cells from wild-type and fetal growth restriction mice, using 10 ng of rRNA-depleted RNA.Genome biologyUli-epic: profiling RNA modifications from ultra-low input samples.PMC1260683021ZR148030082230054324713402021YFA110040082271723Peng YHe WJiang XChen WXu CChang SZhu WHu LWang YKang JfalseUli-epic: profiling RNA modifications from ultra-low input samples.High-throughput sequencing with chemical labeling enables robust, transcriptome-wide detection of RNA modifications at single-nucleotide resolution. However, these methods typically require substantial RNA amounts due to harsh treatments. We introduce Uli-epic, an innovative library construction strategy that enables profiling epitranscriptomic modifications using 100 pg to 1 ng of RNA. Utilizing Uli-epic BID-seq, we investigate pseudouridine (Ψ) sites in neural stem cells and sperm RNA from wild-type and fetal growth restriction mice, using only 500 pg of rRNA-depleted RNA. Uli-epic GLORI quantifies m⁶A in sperm and neural stem cells from wild-type and fetal growth restriction mice, using 10 ng of rRNA-depleted RNA.2025-01-01T00:00:00Z2025 Nov2026-06-05T13:40:22.749Z2026-05-17T03:12:26.834ZS-EPMC126068304121982310.1186/s13059-025-03857-3