GEO series
Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation
GSE220103
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
27 samples
Submitted 2024/07/10
Platform GPL18573
Summary
DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.
Published in
Titus KR, Simandi Z, Chandrashekar H et al.
· Cell genomics 2024
· PMID 38991604
· doi:10.1016/j.xgen.2024.100606
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE220103_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 27 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA908804 and SRA study SRP411365. Searching any of these in the dataset finder brings you back here.
Study design
21 conditions, each sampled once — no replicated groups
iPSC_RNAseq, ×3
NPC_RNAseq, ×3
Neuron_RNAseq, ×3
Read from 27 sample titles: 21 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM6788424 NPC_HiC
- GSM6788425 iPSC_HiC
- GSM6788426 NPC_RNAPII_IP
- GSM6788427 iPS_RNAPII_IP
- GSM6788428 NPC_RNAPII_Input
- GSM6788429 iPS_RNAPII_Input
- GSM6788430 NPC_H3K27ac_IP
- GSM6788431 iPSC_H3K27ac_IP
- GSM6788432 NPC_CTCF_IP
- GSM6788433 iPS_CTCF_IP
- GSM6788437 NPC_CTCF_H3K27ac_Input
- GSM6788438 iPSC_CTCF_H3K27ac_Input
- GSM7688212 Neuron_HiC
- GSM7688213 Neuron_RNAPII_IP
- GSM7688214 Neuron_RNAPII_Input
- GSM7688215 Neuron_H3K27ac_IP
- GSM7688216 Neuron_CTCF_IP
- GSM7688217 Neuron_CTCF_H3K27ac_Input
- GSM7699780 iPSC_RNAseq, rep1
- GSM7699781 iPSC_RNAseq, rep2
- GSM7699782 iPSC_RNAseq, rep3
- GSM7699783 NPC_RNAseq, rep1
- GSM7699784 NPC_RNAseq, rep2
- GSM7699785 NPC_RNAseq, rep3
- GSM7699786 Neuron_RNAseq, rep1
- GSM7699787 Neuron_RNAseq, rep2
- GSM7699788 Neuron_RNAseq, rep3
Similar datasets
- GSE328578 CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL 156 samples
- GSE290367 Single-cell multiomic integration identifies widespread, cell-type resolved fetal reactivation in the diseased human heart 90 samples
- GSE277215 Insights into intestinal neuroendocrine tumors in relation to normal human EEC differentiation 53 samples
- GSE237959 ZBTB48 is a pioneer factor regulating B-cell-specific CIITA expression. 36 samples
- GSE283715 Cerebrospinal fluid-linked periventricular gradient pathology in multiple sclerosis associates with ependymal cell reactivity and cell adhesion disruption 18 samples
- GSE296875 Liver single-nucleus multiome profiling reveals cell-type mechanisms for cardiometabolic traits 16 samples
- GSE309697 Generation of a Comprehensive Epigenomic Atlas in Clear Cell Renal Cell Carcinoma Informs Kidney Cancer Progression and Heritability 265 samples
- GSE303478 Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome 217 samples
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.