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| Status |
Public on May 29, 2024 |
| Title |
MBN_ssDRIP_seq_artificial_hybrid |
| Sample type |
SRA |
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| Source name |
plasmid
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| Organism |
Escherichia coli |
| Characteristics |
cell type: plasmid
pulldown of: DNA:RNA hybrid
treatment: MBN digestion
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| Extracted molecule |
other |
| Extraction protocol |
To prepare RNA:DNA hybrid substrates, oligonucleotides of DNA (5'-ACGTGTCATGACTGACACTGGCAGTACGTAGCAGTGGTAGAACCTTCGTGTGCTTTCGCCAGCCCCAGACGGGTCAGATTTGGCAGATTGAGCGGGCCTTTACGACCGTTATCAGCTTCGCCTTTGGCACAAGCTTCTGCGATATGACCCAGGGTGTCAGCCCCGACGTCACCAAAGCGTTCTGCATCTTCTGTAGCGCCGATGCCGAATGAGTCCAGCACCATCCC
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Library strategy: DRIP-seq
For basic or modified ssDRIP-seq, reads were aligned to the genome with Bowtie 2 (version 2.3.4.2) using default settings. Duplicates were removed by Picard tools (http://broadinstitute.github.io/picard). Using samtools (version 1.3), unmapped reads and reads with more than three mismatches were removed, and the total mapped reads (non-strand R-loops) were divided into wR-loop and cR-loop reads (wR-loop means an R-loop with a Watson strand unpaired ssDNA, while cR-loop means an R-loop with a Crick strand unpaired ssDNA) . Aligned reads files (BAM) were converted to bigWig files by using deepTools (version 2.4.2).
Supplementary files format and content: bigWig
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| Submission date |
Oct 17, 2022 |
| Last update date |
May 29, 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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| Platform ID |
GPL25368 |
| Series (1) |
| GSE183453 |
R-loop landscapes during parental-to-zygotic transition in zebrafish |
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| Relations |
| BioSample |
SAMN31314017 |
| SRA |
SRX17915364 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6645319_MBN_ssDRIP_seq_artificial_hybrid_1stbase.bw |
1.9 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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