|
| Status |
Public on Nov 08, 2023 |
| Title |
Enhancing sensitivity and versatility of Tn5-based single cell omics IV |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
|
| |
|
| Overall design |
Human PBMCs were analyzed by scATAC-seq using 10xTn5 or Tn5hc.
-------------------------------------
Authors state:
For human data, we are in the process of uploading the raw data to EGA. We will provide the EGA accession numbers to you as soon as we obtain them.
|
| |
|
| Contributor(s) |
Seufert I, Rippe K, Mallm J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jun 21, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Isabelle Seufert |
| Organization name |
DKFZ
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (2) |
|
| This SubSeries is part of SuperSeries: |
| GSE235506 |
Enhancing sensitivity and versatility of Tn5-based single cell omics |
|
| Relations |
| BioProject |
PRJNA986160 |
