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| Status |
Public on Jun 08, 2023 |
| Title |
Simultaneous Profiling of Chromatin-Associated RNA at Targeted DNA Loci and RNA-RNA Interactions through TaDRIM-Seq |
| Organisms |
Homo sapiens; Oryza sativa Indica Group |
| Experiment type |
Other
|
| Summary |
The enormous variety of different RNAs are transcribed from eukaryotic genome. Some RNAs, particular long non-coding RNAs (lncRNAs), enrich on chromatin via transcribed RNAs to retain at their transcription site (Cis-acting RNAs) and recruited to different genomic regions (Trans-acting RNAs), which play significant roles in regulating gene transcription, epigenomic modifications and mediating chromatin states. Here, we developed TaDRIM-Seq (Targeted DNA-associated RNA and RNA-RNA Interactions Mapping by Sequencing) method to capture RNA-DNA on specific protein region and RNA-RNA spatial interactions in nuclei. We performed TaDRIM-Seq of antibodies H3, H3K9ac and H3K27me3 in rice and H3K4me3 and CTCF in human K562 cells, to identify chromatin-interacting RNAs and RNA-RNA interactions.
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| Overall design |
We report TaDRIM-Seq technique PG-Tn5-mediated targeted DNA element and proximity ligation to simultaneously detect chromatin-associated RNAs in diverse regions of the genome and RNA-RNA spatial interactions in nuclei.
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| Contributor(s) |
Ding C, Chen G |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jun 06, 2023 |
| Last update date |
Jun 12, 2024 |
| Contact name |
guoting chen |
| E-mail(s) |
chenguoting@webmail.hzau.edu.cn
|
| Phone |
+86 13212791520
|
| Organization name |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
1 Shizishan Street, Hongshan District
|
| City |
Wuhan |
| ZIP/Postal code |
430000 |
| Country |
China |
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| Platforms (2) |
| GPL20795 |
HiSeq X Ten (Homo sapiens) |
| GPL26667 |
HiSeq X Ten (Oryza sativa Indica Group) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA980586 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE234228_AM_GSE234228_H3K9ac_DNA-RNA-interaction.bedpe.gz |
18.1 Mb |
(ftp)(http) |
BEDPE |
| GSE234228_AM_RNA-RNA-interaction.bedpe.gz |
4.1 Mb |
(ftp)(http) |
BEDPE |
| GSE234228_CTCF_DNA-RNA-interaction.bedpe.gz |
1.9 Mb |
(ftp)(http) |
BEDPE |
| GSE234228_H3K27me3_DNA-RNA-interaction.bedpe.gz |
11.7 Mb |
(ftp)(http) |
BEDPE |
| GSE234228_H3K4me3_DNA-RNA-interaction.bedpe.gz |
18.2 Mb |
(ftp)(http) |
BEDPE |
| GSE234228_K562-cell_RNA-RNA-interaction.bedpe.gz |
15.8 Mb |
(ftp)(http) |
BEDPE |
| GSE234228_PM_GSE234228_H3K9ac_DNA-RNA-interaction.bedpe.gz |
24.2 Mb |
(ftp)(http) |
BEDPE |
| GSE234228_PM_RNA-RNA-interaction.bedpe.gz |
740.5 Kb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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