GEO series
scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [cellline_scHiCAR]
Summary
The three-dimensional (3D) organization of cis-regulatory elements (CREs) plays a central role in transcription control. However, capturing transcriptome, epigenome, and 3D genome from the same single cells remains technically challenging. Here, we present scHiCAR (single-cell Hi-C with ATAC and RNA-seq), a combinatorial barcoding-based method that simultaneously profiles mRNA, open chromatin, and chromosome-conformation-capture from the same cells. Compared to existing single-cell 3D genome methods, scHiCAR more efficiently enriches long-range cis-interactions anchored at candidate CREs (cCREs). Applied to 1.62 million mouse brain cells and complemented with a deep learning-based loop caller, scHiCAR accurately defines cell-type-specific transcriptomes, accessible cCREs, and 5kb-resolution enhancer-promoter pairs across 22 brain cell types. scHiCAR also performs robustly in challenging tissues such as skeletal muscle, enabling tri-modal single-cell level analysis of gene regulation dynamics during muscle stem cell regeneration. scHiCAR offers a scalable, efficient, and cost-effective platform for studying gene regulatory landscapes in complex tissues at single-cell resolution.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE267117_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 34 samples.
Also filed as BioProject PRJNA1109789. Searching any of these in the dataset finder brings you back here.
Study design
32 × human H1, GM12878 and mouse ESC, DNA, batch1, vs 2 × human H1, GM12878 and mouse ESC, RNA, batch2,
Supports a between-group comparison across 34 samples.
2 replicated groups read from 34 sample titles; they account for 34 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8260157 human H1, GM12878 and mouse ESC, DNA, batch1, rep1
- GSM8260158 human H1, GM12878 and mouse ESC, DNA, batch1, rep2
- GSM8260159 human H1, GM12878 and mouse ESC, DNA, batch1, rep3
- GSM8260160 human H1, GM12878 and mouse ESC, DNA, batch1, rep4
- GSM8260161 human H1, GM12878 and mouse ESC, DNA, batch1, rep5
- GSM8260162 human H1, GM12878 and mouse ESC, DNA, batch1, rep6
- GSM8260163 human H1, GM12878 and mouse ESC, DNA, batch1, rep7
- GSM8260164 human H1, GM12878 and mouse ESC, DNA, batch1, rep8
- GSM8260165 human H1, GM12878 and mouse ESC, DNA, batch1, rep9
- GSM8260166 human H1, GM12878 and mouse ESC, DNA, batch1, rep10
- GSM8260167 human H1, GM12878 and mouse ESC, DNA, batch1, rep11
- GSM8260168 human H1, GM12878 and mouse ESC, DNA, batch1, rep12
- GSM8260169 human H1, GM12878 and mouse ESC, DNA, batch1, rep13
- GSM8260170 human H1, GM12878 and mouse ESC, DNA, batch1, rep14
- GSM8260171 human H1, GM12878 and mouse ESC, DNA, batch1, rep15
- GSM8260172 human H1, GM12878 and mouse ESC, DNA, batch1, rep16
- GSM8260173 human H1, GM12878 and mouse ESC, DNA, batch1, rep17
- GSM8260174 human H1, GM12878 and mouse ESC, DNA, batch1, rep18
- GSM8260175 human H1, GM12878 and mouse ESC, DNA, batch1, rep19
- GSM8260176 human H1, GM12878 and mouse ESC, DNA, batch1, rep20
- GSM8260177 human H1, GM12878 and mouse ESC, DNA, batch1, rep21
- GSM8260178 human H1, GM12878 and mouse ESC, DNA, batch1, rep22
- GSM8260179 human H1, GM12878 and mouse ESC, DNA, batch1, rep23
- GSM8260180 human H1, GM12878 and mouse ESC, DNA, batch1, rep24
- GSM8260181 human H1, GM12878 and mouse ESC, DNA, batch1, rep25
- GSM8260182 human H1, GM12878 and mouse ESC, DNA, batch1, rep26
- GSM8260183 human H1, GM12878 and mouse ESC, DNA, batch1, rep27
- GSM8260184 human H1, GM12878 and mouse ESC, DNA, batch1, rep28
- GSM8260185 human H1, GM12878 and mouse ESC, DNA, batch1, rep29
- GSM8260186 human H1, GM12878 and mouse ESC, DNA, batch1, rep30
- GSM8260187 human H1, GM12878 and mouse ESC, DNA, batch1, rep31
- GSM8260188 human H1, GM12878 and mouse ESC, DNA, batch1, rep32
- GSM8260189 human H1, GM12878 and mouse ESC, RNA, batch2, rep1
- GSM8260190 human H1, GM12878 and mouse ESC, RNA, batch2, rep2
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