 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| E-mail(s) |
lir4@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platforms (1) |
|
| Samples (13)
|
|
| Relations |
| BioProject |
PRJNA694671 |
| SRA |
SRP303191 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...