GEO series
Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [ChIP-Seq]
GSE337829
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
32 samples
Submitted 2026/07/07
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
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Direct links to NCBI, no account and no request form: the whole study as GSE337829_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 32 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1491292 and SRA study SRP715947. Searching any of these in the dataset finder brings you back here.
Study design
12 conditions, mostly in duplicate
GBM8_ChIPseq_H3K27Ac_after_CRISPRi ×2
GBM8_ChIPseq_H3K27Me3_after_CRISPRi ×2
GBM8_ChIPseq_H3K27Ac_before_CRISPRi ×2
GBM8_ChIPseq_H3K27Me3_before_CRISPRi ×2
GBM8_ChIPseq_PPARD ×2
NHA_ChIPseq_H3K27AC_after_CRISPRi ×2
NHA_ChIPseq_H3K27Me3_after_CRISPRi ×2
NHA_ChIPseq_H3K27AC_before_CRISPRi ×2
+12 more
Supports a between-group comparison across 24 samples.
12 replicated groups read from 32 sample titles; they account for 24 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9861127 GBM8_ChIPseq_Input_after_CRISPRi
- GSM9861128 GBM8_ChIPseq_H3K27Ac_after_CRISPRi_rep1
- GSM9861129 GBM8_ChIPseq_H3K27Ac_after_CRISPRi_rep2
- GSM9861130 GBM8_ChIPseq_H3K27Me3_after_CRISPRi_rep1
- GSM9861131 GBM8_ChIPseq_H3K27Me3_after_CRISPRi_rep2
- GSM9861132 GBM8_ChIPseq_Input_before_CRISPRi
- GSM9861133 GBM8_ChIPseq_H3K27Ac_before_CRISPRi_rep1
- GSM9861134 GBM8_ChIPseq_H3K27Ac_before_CRISPRi_rep2
- GSM9861135 GBM8_ChIPseq_H3K27Me3_before_CRISPRi_rep1
- GSM9861136 GBM8_ChIPseq_H3K27Me3_before_CRISPRi_rep2
- GSM9861137 GBM8_ChIPseq_Input
- GSM9861138 GBM8_ChIPseq_PPARD_rep1
- GSM9861139 GBM8_ChIPseq_PPARD_rep2
- GSM9861140 NHA_ChIPseq_Input_after_CRISPRi
- GSM9861141 NHA_ChIPseq_H3K27AC_after_CRISPRi_rep_1
- GSM9861142 NHA_ChIPseq_H3K27AC_after_CRISPRi_rep_2
- GSM9861143 NHA_ChIPseq_H3K27Me3_after_CRISPRi_rep1
- GSM9861144 NHA_ChIPseq_H3K27Me3_after_CRISPRi_rep2
- GSM9861145 NHA_ChIPseq_Input_before_CRISPRi
- GSM9861146 NHA_ChIPseq_H3K27AC_before_CRISPRi_rep_1
- GSM9861147 NHA_ChIPseq_H3K27AC_before_CRISPRi_rep_2
- GSM9861148 NHA_ChIPseq_H3K27Me3_before_CRISPRi_rep1
- GSM9861149 NHA_ChIPseq_H3K27Me3_before_CRISPRi_rep2
- GSM9861150 NHA_ChIPseq_Input_DMSO
- GSM9861151 NHA_ChIPseq_PPARD_DMSO_rep1
- GSM9861152 NHA_ChIPseq_PPARD_DMSO_rep2
- GSM9861153 NHA_ChIPseq_Input_RA_12h
- GSM9861154 NHA_ChIPseq_PPARD_RA_12h_rep1
- GSM9861155 NHA_ChIPseq_PPARD_RA_12h_rep2
- GSM9861156 NHA_ChIPseq_Input_RA_24h
- GSM9861157 NHA_ChIPseq_PPARD_RA_24h_rep1
- GSM9861158 NHA_ChIPseq_PPARD_RA_24h_rep2
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