NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE223917 Query DataSets for GSE223917
Status Public on Jan 31, 2023
Title Linking genome structures to functions during lineage specification by simultaneous single-cell Hi-C and RNA-seq simultaneous single-cell Hi-C and RNA-seq
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary Remarkable progress has been made recently in single-cell chromosome conformation capture technologies. However, a method that allows simultaneous profiling of chromatin architecture and gene expression has not been reported. Here we developed an assay named Hi-C and RNA-seq employed simultaneously (HiRES) and performed it on thousands of single cells from developing mouse embryos. Single-cell 3D genome structures, despite being heavily determined by the cell cycle and developmental stages, gradually diverged in a cell-type-specific manner as development progressed. We further developed a computational pipeline to identify and link differential chromatin interactions to their relevant genes based on covariation of interaction strength and transcription activity. By comparing the pseudo temporal dynamics of chromatin interactions with gene expression, we found a widespread chromatin rewiring that occurred prior to transcription activation. Our results demonstrate that the establishment of specific chromatin interactions are tightly related to transcriptional control and cell functions during lineage specification.
 
Overall design Using Hi-C and RNA-seq to analyze single cells from mouse embryos and mouse brains.
Web link https://www.science.org/doi/10.1126/science.adg3797
 
Contributor(s) Liu , Chen Y, Xia Q
Citation(s) 37289875
BioProject PRJNA907173
Submission date Jan 28, 2023
Last update date Jul 05, 2023
Contact name Zhiyuan Liu
E-mail(s) lemonhhh1030@gmail.com
Phone 18818223086
Organization name Peking University
Street address Yiheyuan Road
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (7895)
GSM6998595 Mouse, embryos, cell-GasaE751001
GSM6998596 Mouse, embryos, cell-GasaE751002
GSM6998597 Mouse, embryos, cell-GasaE751003

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE223917_HiRES_brain.rna.umicount.tsv.gz 3.4 Mb (ftp)(http) TSV
GSE223917_HiRES_brain_metadata.xlsx 84.1 Kb (ftp)(http) XLSX
GSE223917_HiRES_emb.rna.umicount.tsv.gz 36.2 Mb (ftp)(http) TSV
GSE223917_HiRES_emb_GADIs.tsv.gz 14.1 Mb (ftp)(http) TSV
GSE223917_HiRES_emb_metadata.xlsx 1.7 Mb (ftp)(http) XLSX
GSE223917_HiRES_emb_residuals-updated-02-22-2023.tsv.gz 7.4 Mb (ftp)(http) TSV
GSE223917_HiRES_emb_significant_DIs.tsv.gz 191.2 Mb (ftp)(http) TSV
GSE223917_RAW.tar 75.0 Gb (http)(custom) TAR (of PAIRS, TXT)
GSE223917_brain_genome1.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE223917_brain_genome2.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE223917_embryo_genome1.tsv.gz 21.1 Mb (ftp)(http) TSV
GSE223917_embryo_genome2.tsv.gz 20.5 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap