GEO series
Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids]
GSE337246
Homo sapiens
Expression profiling by high throughput sequencing
35 samples
Submitted 2026/07/08
Platform GPL16791
Summary
The human genome is pervasively transcribed into protein-coding and regulatory non-coding RNAs whose functions are coordinated within higher-order nuclear architectures. However, direct mapping of RNA–RNA and DNA–DNA interaction networks in complex human tissues at single-cell resolution has remained a major challenge. Here, we present SCIENCE-seq, a multimodal single-cell interactomics platform enabling simultaneous detection of RNA–RNA interactions and chromatin DNA–DNA contacts within individual cells. Applied to primary glioma specimens, SCIENCE-seq reveals cancer-specific interactions organized by lncRNAs and centered on key oncogenic drivers, including EGFR, hTERT, SOX2, CDK6, CDC42, CD47, and HOX loci. These datasets uncover previously unrecognized molecular relationships between premature lncRNAs and pre-mRNAs that regulate transcription, alternative splicing, and polyadenylation. Notably, we identify a glioma-specific trans-chromosomal HOX hub driven by five interacting lncRNAs. Targeting these RNA and DNA interactions with steric antisense oligonucleotides (ASOs) or CRISPRi enables selective inhibition of oncogenic programs in malignant cells while sparing normal tissue, establishing chromatin interactomes as actionable therapeutic targets.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE337246_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 35 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1484556 and SRA study SRP714370. Searching any of these in the dataset finder brings you back here.
Study design
5 conditions, mostly with about 7 replicates each
scRNAseq_organoids_CD47_ASO_treatment ×7
scRNAseq_organoids_CDC42_ASO_treatment ×7
scRNAseq_organoids_Control_ASO_treatment ×7
scRNAseq_organoids_LINC01116_ASO_treatment ×7
scRNAseq_organoids_SOX2_ASO_treatment ×7
Supports a between-group comparison across 35 samples.
5 replicated groups read from 35 sample titles; they account for 35 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9851593 scRNAseq_organoids_CD47_ASO_treatment_1
- GSM9851594 scRNAseq_organoids_CD47_ASO_treatment_2
- GSM9851595 scRNAseq_organoids_CD47_ASO_treatment_3
- GSM9851596 scRNAseq_organoids_CD47_ASO_treatment_4
- GSM9851597 scRNAseq_organoids_CD47_ASO_treatment_5
- GSM9851598 scRNAseq_organoids_CD47_ASO_treatment_6
- GSM9851599 scRNAseq_organoids_CD47_ASO_treatment_7
- GSM9851600 scRNAseq_organoids_CDC42_ASO_treatment_1
- GSM9851606 scRNAseq_organoids_CDC42_ASO_treatment_2
- GSM9851608 scRNAseq_organoids_CDC42_ASO_treatment_3
- GSM9851609 scRNAseq_organoids_CDC42_ASO_treatment_4
- GSM9851610 scRNAseq_organoids_CDC42_ASO_treatment_5
- GSM9851611 scRNAseq_organoids_CDC42_ASO_treatment_6
- GSM9851612 scRNAseq_organoids_CDC42_ASO_treatment_7
- GSM9851613 scRNAseq_organoids_Control_ASO_treatment_1
- GSM9851614 scRNAseq_organoids_Control_ASO_treatment_2
- GSM9851615 scRNAseq_organoids_Control_ASO_treatment_3
- GSM9851616 scRNAseq_organoids_Control_ASO_treatment_4
- GSM9851617 scRNAseq_organoids_Control_ASO_treatment_5
- GSM9851618 scRNAseq_organoids_Control_ASO_treatment_6
- GSM9851619 scRNAseq_organoids_Control_ASO_treatment_7
- GSM9851620 scRNAseq_organoids_LINC01116_ASO_treatment_1
- GSM9851621 scRNAseq_organoids_LINC01116_ASO_treatment_2
- GSM9851622 scRNAseq_organoids_LINC01116_ASO_treatment_3
- GSM9851623 scRNAseq_organoids_LINC01116_ASO_treatment_4
- GSM9851624 scRNAseq_organoids_LINC01116_ASO_treatment_5
- GSM9851625 scRNAseq_organoids_LINC01116_ASO_treatment_6
- GSM9851626 scRNAseq_organoids_LINC01116_ASO_treatment_7
- GSM9851627 scRNAseq_organoids_SOX2_ASO_treatment_1
- GSM9851628 scRNAseq_organoids_SOX2_ASO_treatment_2
- GSM9851629 scRNAseq_organoids_SOX2_ASO_treatment_3
- GSM9851630 scRNAseq_organoids_SOX2_ASO_treatment_4
- GSM9851631 scRNAseq_organoids_SOX2_ASO_treatment_5
- GSM9851632 scRNAseq_organoids_SOX2_ASO_treatment_6
- GSM9851633 scRNAseq_organoids_SOX2_ASO_treatment_7
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