 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 12, 2024 |
| Title |
mDRIP-seq: a high-throughput method for R-loop mapping and quantitative assessment. |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Current methods for R-loop mapping need to perform DNA:RNA immunoprecipitation for each sample individually, with consequent limitations in throughput. Here, we develop and validate mDRIP-seq, a multi-sample barcoding and pooling method for R-loop mapping. We show mDRIP-seq performs equivalently as conventional methods, but with the merits of high throughput and cost-efficiency. We also show the simplicity of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. Together, mDRIP-seq is a high-throughput and cost-efficient method for R-loop mapping and quantitative assessment and can be widely applied to large-scale dynamic profiles of these important structures for diverse organisms.
|
| |
|
| Overall design |
mDRIP-seq development, and R-loop mapping in multiple samples
|
| |
|
| Contributor(s) |
Sun C, Xu W |
| Citation(s) |
38821747 |
| |
| Submission date |
Oct 27, 2023 |
| Last update date |
Sep 12, 2024 |
| Contact name |
Changbin Sun |
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Department |
Agricultural Genomics Institute at Shenzhen
|
| Lab |
Guangdong Laboratory of Lingnan Modern Agriculture
|
| Street address |
Dapeng
|
| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL27812 |
Illumina NovaSeq 6000 (Saccharomyces cerevisiae) |
|
| Samples (20)
|
| GSM7868672 |
def1Δ, rep1 |
| GSM7868673 |
def1Δ, rep2 |
| GSM7868674 |
def1Δ, rep3 |
| GSM7868675 |
dhh1Δ, rep1 |
| GSM7868676 |
dhh1Δ, rep2 |
| GSM7868677 |
med1Δ, rep1 |
| GSM7868678 |
med1Δ, rep2 |
| GSM7868679 |
nam7Δ, rep1 |
| GSM7868680 |
nam7Δ, rep2 |
| GSM7868681 |
rad51Δ, rep1 |
| GSM7868682 |
rad51Δ, rep2 |
| GSM7868683 |
snf2Δ, rep1 |
| GSM7868684 |
snf2Δ, rep2 |
| GSM7868685 |
snf5Δ, rep1 |
| GSM7868686 |
snf5Δ, rep2 |
| GSM7868687 |
snf6Δ, rep1 |
| GSM7868688 |
snf6Δ, rep2 |
|
| This SubSeries is part of SuperSeries: |
| GSE219071 |
mDRIP-seq is a high-throughput method for quantitative R-loop landscape profiling |
|
| Relations |
| BioProject |
PRJNA1032915 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE246423_rawCount.txt.gz |
286.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...