GEO series
Sensitive monitoring of enhancer and noncoding RNA transcription via ribozyme-assisted RNA editing
GSE315648
Homo sapiens; Mus musculus
Other; Expression profiling by high throughput sequencing
71 samples
Submitted 2026/03/13
Platform GPL24676Platform GPL28330Platform GPL29480
Summary
The primary goal of this study is to provide tools for understanding transcriptional regulation of native genomic elements that combine high sensitivity, quantitative output, and broad applicability. Existing methods often have limited dynamic range, disrupt host RNAs, or fail to detect short-lived transcripts. Here, we present ribozyme-processed ADAR-engaging RNA-directed editing (REDDIT), a technology that converts transcriptional events into reporter protein translation via precise A-to-I RNA editing. REDDIT sensitively detects transcription from protein-coding genes, long noncoding RNAs (lncRNAs), primary microRNAs (pri-miRNAs), and enhancer RNAs (eRNAs), including low abundance and short-lived species, while minimally perturbing host gene expression, RNA processing, and the global editome. We apply REDDIT to monitor the naïve-to-primed transition in human embryonic stem cells (hESCs) and convert it into a transcription recorder that permanently logs transient and combinatorial transcriptional inputs when paired with Cre recombinase. Finally, by adapting REDDIT for high-throughput screening, we uncover multiple signaling pathways that regulate lncRNA and eRNA biogenesis. REDDIT therefore provides a scalable platform for quantitative monitoring and retrospective analysis of endogenous transcriptional dynamics across diverse genomic contexts.
Published in
Wang J, Wang JZ, Hu LF et al.
· Nature communications 2026
· PMID 41997976
· doi:10.1038/s41467-026-72033-3
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE315648_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 71 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1398389 and SRA study SRP659834. Searching any of these in the dataset finder brings you back here.
Study design
20 conditions, mostly in duplicate
REDDIT_hESC_ctrl ×2
REDDIT_NANOG ×2
REDDIT_MIR302 ×2
REDDIT_ACTB_intron1 ×2
REDDIT_ACTB_polyA ×2
REDDIT_SOX2_polyA ×2
REDDIT_mESC_Ctrl ×2
REDDIT_Lncenc1 ×2
+12 more
Supports a between-group comparison across 40 samples.
20 replicated groups read from the first 40 of 71 sample titles; they account for 40 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9433925 REDDIT_hESC_ctrl_rep1
- GSM9433926 REDDIT_hESC_ctrl_rep2
- GSM9433927 REDDIT_NANOG_rep1
- GSM9433928 REDDIT_NANOG_rep2
- GSM9433929 REDDIT_MIR302_rep1
- GSM9433930 REDDIT_MIR302_rep2
- GSM9433931 REDDIT_ACTB_intron1_rep1
- GSM9433932 REDDIT_ACTB_intron1_rep2
- GSM9433933 REDDIT_ACTB_polyA_rep1
- GSM9433934 REDDIT_ACTB_polyA_rep2
- GSM9433935 REDDIT_SOX2_polyA_rep1
- GSM9433936 REDDIT_SOX2_polyA_rep2
- GSM9433937 REDDIT_mESC_Ctrl_rep1
- GSM9433938 REDDIT_mESC_Ctrl_rep2
- GSM9433939 REDDIT_Lncenc1_rep1
- GSM9433940 REDDIT_Lncenc1_rep2
- GSM9433941 MIR302_Dif_D0_rep1
- GSM9433942 MIR302_Dif_D0_rep2
- GSM9433943 MIR302_Dif_D5_rep1
- GSM9433944 MIR302_Dif_D5_rep2
- GSM9433945 MIR302_Dif_D12_rep1
- GSM9433946 MIR302_Dif_D12_rep2
- GSM9433947 MIR302_Dif_D20_rep1
- GSM9433948 MIR302_Dif_D20_rep2
- GSM9433949 MIR302_Dif_D14_high_rep1
- GSM9433950 MIR302_Dif_D14_high_rep2
- GSM9433951 MIR302_Dif_D14_low_rep1
- GSM9433952 MIR302_Dif_D14_low_rep2
- GSM9433953 WT_mESC_DMSO_7days_rep1
- GSM9433954 WT_mESC_DMSO_7days_rep2
- GSM9433955 WT_mESC_UNC0638_7days_rep1
- GSM9433956 WT_mESC_UNC0638_7days_rep2
- GSM9433957 WT_mESC_DMSO_48h_rep1
- GSM9433958 WT_mESC_DMSO_48h_rep2
- GSM9433959 WT_mESC_UNC0638_48h_rep1
- GSM9433960 WT_mESC_UNC0638_48h_rep2
- GSM9433961 WT_hESC_DMSO_rep1
- GSM9433962 WT_hESC_DMSO_rep2
- GSM9433963 WT_hESC_RepSox_rep1
- GSM9433964 WT_hESC_RepSox_rep2
+ 31 more — browse all 71 samples with per-sample file links →
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