GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE165478 Query DataSets for GSE165478
Status Public on Jun 21, 2021
Title Low-input ATAC&mRNA-Seq: a simple and robust method for simultaneous dual-omics profiling with low cell number
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Deciphering epigenetic regulation of gene expression requires measuring the epigenome and transcriptome jointly. However, multi-omics profiling remains challenging for low-input samples. Therefore, we developed low-input ATAC&mRNA-Seq, a simple and robust method for studying the role of chromatin structure in gene regulation in a single experiment with thousands of cells, to maximize insights from limited input material by obtaining ATAC-seq and mRNA-seq data simultaneously from the same cells with data quality comparable to conventional mono-omics assays. Remarkably, integrative data analysis revealed similar strong association between promoter accessibility and gene expression using the data of low-input ATAC&mRNA-Seq as using single-assayed data, underscoring the accuracy and reliability of our dual-omics assay to generate both data types simultaneously with just thousands of cells. We envision our method to be widely applied in many biological disciplines with limited materials.
Overall design Low-input ATAC&mRNA-Seq was performed on E14 mESCs with 5K, 10K, and 20K cells. Two independent experiments were carried out on different days to assess data reproducibility. To benchmark our method, Omni-ATAC-seq was also conducted with 5K, 10K, and 50K of E14 mESCs.
Contributor(s) Li R, Grimm SA
Citation(s) 34414388, 34485936
Submission date Jan 25, 2021
Last update date Sep 08, 2021
Contact name ruifang li
Organization name NIEHS
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (13)
GSM5034381 ATAC-5K-exp2
GSM5034382 ATAC-10K-exp1
GSM5034383 ATAC-10K-exp2
BioProject PRJNA694671
SRA SRP303191

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
GSE165478_RAW.tar 2.1 Gb (http)(custom) TAR (of BED, BIGWIG)
GSE165478_RNAseq_counts_per_gene.txt.gz 570.4 Kb (ftp)(http) TXT
GSE165478_unified_ATAC_peaks.bed.gz 244.3 Kb (ftp)(http) BED
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