GEO series
Genome-wide DNA replication profiling and full-length total RNA sequencing from the same single cell [hTERT-RPE1 Whole-S]
GSE278951
Homo sapiens
Expression profiling by high throughput sequencing; Other
98 samples
Submitted 2025/08/27
Platform GPL20795
Summary
Single-cell sequencing has advanced our understanding of cell-type diversity and heterogeneity. However, existing single-cell multi-omics methods lack DNA data resolution and full-length total RNA detection. Here, we introduce single-cell (sc)Repli-RamDA-seq (scRR-seq), a novel multi-omics method that enables high-resolution DNA replication profiling and full-length total RNA sequencing from the same single cell, made possible by the clean separation of DNA and RNA. scRR-seq generates DNA replication and RNA sequencing data comparable to individually obtained scRepli-seq and scRamDA-seq data, respectively. scRR-seq also allows one to tell the cell-cycle stage of a given S-phase cell and detects copy-number variation (CNV) in non-S-phase cells. scRR-seq outperforms other scRNA-seq methods in the number of transcripts identified and full-length total RNA detection. Furthermore, scRR-seq allowed haplotype-specific analysis and the identification of novel S-phase markers. Taken together, scRR-seq is a robust single-cell multi-omics method with promising potential for comprehensive genome and transcriptome analysis.
Published in
Poonperm R, Yoneda T, Imada T et al.
· Nature communications 2025
· PMID 41397953
· doi:10.1038/s41467-025-64688-1
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE278951_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 98 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1169832 and SRA study SRP536989. Searching any of these in the dataset finder brings you back here.
Study design
24 × RNA_RPE1_scRR1_Lot2_WholeS vs 9 × RNA_RPE1_scRR1_Lot1_WholeS vs 6 × RNA_RPE1_scRR3_Lot1_WholeS
Supports a between-group comparison across 39 samples.
3 replicated groups read from the first 40 of 98 sample titles; they account for 39 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8558477 RNA_RPE1_scRR1_Lot1_WholeS_013
- GSM8558478 RNA_RPE1_scRR1_Lot1_WholeS_014
- GSM8558479 RNA_RPE1_scRR1_Lot1_WholeS_015
- GSM8558480 RNA_RPE1_scRR1_Lot1_WholeS_016
- GSM8558481 RNA_RPE1_scRR1_Lot1_WholeS_003
- GSM8558482 RNA_RPE1_scRR1_Lot1_WholeS_005
- GSM8558483 RNA_RPE1_scRR1_Lot1_WholeS_006
- GSM8558484 RNA_RPE1_scRR1_Lot1_WholeS_007
- GSM8558485 RNA_RPE1_scRR1_Lot1_WholeS_008
- GSM8558486 RNA_RPE1_scRR1_Lot2_WholeS_011
- GSM8558487 RNA_RPE1_scRR1_Lot2_WholeS_016
- GSM8558488 RNA_RPE1_scRR1_Lot2_WholeS_002
- GSM8558489 RNA_RPE1_scRR1_Lot2_WholeS_020
- GSM8558490 RNA_RPE1_scRR1_Lot2_WholeS_024
- GSM8558491 RNA_RPE1_scRR1_Lot2_WholeS_026
- GSM8558492 RNA_RPE1_scRR1_Lot2_WholeS_028
- GSM8558493 RNA_RPE1_scRR1_Lot2_WholeS_031
- GSM8558494 RNA_RPE1_scRR1_Lot2_WholeS_035
- GSM8558495 RNA_RPE1_scRR1_Lot2_WholeS_037
- GSM8558496 RNA_RPE1_scRR1_Lot2_WholeS_004
- GSM8558497 RNA_RPE1_scRR1_Lot2_WholeS_043
- GSM8558498 RNA_RPE1_scRR1_Lot2_WholeS_044
- GSM8558499 RNA_RPE1_scRR1_Lot2_WholeS_045
- GSM8558500 RNA_RPE1_scRR1_Lot2_WholeS_048
- GSM8558501 RNA_RPE1_scRR1_Lot2_WholeS_049
- GSM8558502 RNA_RPE1_scRR1_Lot2_WholeS_051
- GSM8558503 RNA_RPE1_scRR1_Lot2_WholeS_054
- GSM8558504 RNA_RPE1_scRR1_Lot2_WholeS_058
- GSM8558505 RNA_RPE1_scRR1_Lot2_WholeS_064
- GSM8558506 RNA_RPE1_scRR1_Lot2_WholeS_066
- GSM8558507 RNA_RPE1_scRR1_Lot2_WholeS_070
- GSM8558508 RNA_RPE1_scRR1_Lot2_WholeS_074
- GSM8558509 RNA_RPE1_scRR1_Lot2_WholeS_095
- GSM8558510 RNA_RPE1_scRR3_Lot1_WholeS_013
- GSM8558511 RNA_RPE1_scRR3_Lot1_WholeS_019
- GSM8558512 RNA_RPE1_scRR3_Lot1_WholeS_003
- GSM8558513 RNA_RPE1_scRR3_Lot1_WholeS_006
- GSM8558514 RNA_RPE1_scRR3_Lot1_WholeS_007
- GSM8558515 RNA_RPE1_scRR3_Lot1_WholeS_009
- GSM8558516 RNA_RPE1_scRR3_Lot2_WholeS_011
+ 58 more — browse all 98 samples with per-sample file links →
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