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| Status |
Public on May 29, 2024 |
| Title |
R-loop landscapes during parental-to-zygotic transition in zebrafish |
| Organisms |
Escherichia coli; Arabidopsis thaliana; Danio rerio; synthetic construct |
| Experiment type |
Other
Expression profiling by high throughput sequencing
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| Summary |
The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.
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| Overall design |
ULI-ssDRIP-seq development, and R-loop profiling in zebrafish
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| Contributor(s) |
Xu W, Chen L, Li J, Li K, Sun C, Meng A, Sun Q |
| Citation(s) |
38974143 |
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| Submission date |
Sep 05, 2021 |
| Last update date |
Aug 30, 2024 |
| Contact name |
li kuan |
| E-mail(s) |
likuan@cibr.ac.cn
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| Organization name |
Tsinghua University
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| Street address |
zhongguancun
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (4)
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| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
| GPL25368 |
Illumina NovaSeq 6000 (Escherichia coli) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
| GPL26526 |
Illumina NovaSeq 6000 (synthetic construct) |
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| Samples (60)
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| GSM5557849 |
Arabidopsis thaliana, dsF_ssDRIP_seq |
| GSM5557850 |
Arabidopsis thaliana, dsD_ssDRIP_seq |
| GSM5557852 |
Zebrafish, 10c |
| GSM5557853 |
Zebrafish, 100c |
| GSM5557854 |
Zebrafish, 1kc |
| GSM5557855 |
Zebrafish, 10kc |
| GSM5557856 |
Zebrafish, RNaseH |
| GSM5557857 |
Zebrafish, 500kc_ssDRIP_seq |
| GSM5557858 |
Zebrafish, Oocyte1 |
| GSM5557859 |
Zebrafish, Oocyte2 |
| GSM5557860 |
Zebrafish, Sperm1 |
| GSM5557861 |
Zebrafish, Sperm2 |
| GSM5557862 |
Zebrafish, 4Cell1 |
| GSM5557863 |
Zebrafish, 4Cell2 |
| GSM5557864 |
Zebrafish, 256Cell1 |
| GSM5557865 |
Zebrafish, 256Cell2 |
| GSM5557866 |
Zebrafish, Dome1 |
| GSM5557867 |
Zebrafish, Dome2 |
| GSM5557868 |
Zebrafish, Muscle1 |
| GSM5557869 |
Zebrafish, Muscle2 |
| GSM5557870 |
Zebrafish, Input_Oocyte1 |
| GSM5557871 |
Zebrafish, Input_Oocyte2 |
| GSM5557872 |
Zebrafish, Input_Sperm1 |
| GSM5557873 |
Zebrafish, Input_Sperm2 |
| GSM5557874 |
Zebrafish, Input_4Cell1 |
| GSM5557875 |
Zebrafish, Input_4Cell2 |
| GSM5557876 |
Zebrafish, Input_256Cell1 |
| GSM5557877 |
Zebrafish, Input_256Cell2 |
| GSM5557878 |
Zebrafish, Input_Dome1 |
| GSM5557879 |
Zebrafish, Input_Dome2 |
| GSM5557880 |
Zebrafish, Input_Muscle1 |
| GSM5557881 |
Zebrafish, Input_Muscle2 |
| GSM6165454 |
Zebrafish, GFP, dome, RNA-seq, Rep1 |
| GSM6165455 |
Zebrafish, GFP, dome, RNA-seq, Rep2 |
| GSM6165456 |
Zebrafish, hRNaseH1, dome, RNA-seq, Rep1 |
| GSM6165457 |
Zebrafish, hRNaseH1, dome, RNA-seq, Rep2 |
| GSM6645319 |
MBN_ssDRIP_seq_artificial_hybrid |
| GSM7444947 |
Pol_II_ChIPseq_GFP |
| GSM7444948 |
Pol_II_ChIPseq_hRNaseH1GFP |
| GSM7444949 |
ULI-GFP-dome-1 |
| GSM7444950 |
ULI-GFP-dome-2 |
| GSM7444951 |
ULI-RNH-dome-1 |
| GSM7444952 |
ULI-RNH-dome-2 |
| GSM7444953 |
ULI-stdMO-1 |
| GSM7444954 |
ULI-stdMO-2 |
| GSM7444955 |
ULI-rnaseh1MO-1 |
| GSM7444956 |
ULI-rnaseh1MO-2 |
| GSM7444957 |
RNAseq_StdMO |
| GSM7444958 |
RNAseq_rnaseh1MO |
| GSM8091636 |
MBN_artificial_R_loop |
| GSM8091637 |
S1_artificial_R_loop |
| GSM8091638 |
dsDNase_artificial_R_loop |
| GSM8091639 |
dsFragmentase_artificial_R_loop |
| GSM8091640 |
std_MO_dome_rH2AX_stacc_seq_rep1 |
| GSM8091641 |
std_MO_dome_rH2AX_stacc_seq_rep2 |
| GSM8091642 |
rnaseh1_MO_dome_rH2AX_stacc_seq_rep1 |
| GSM8091643 |
rnaseh1_MO_dome_rH2AX_stacc_seq_rep2 |
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| Relations |
| BioProject |
PRJNA760904 |
| SRA |
SRP335733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE183453_RAW.tar |
4.4 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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