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| Status |
Public on Jan 17, 2024 |
| Title |
Rice K+PDS_rep1 |
| Sample type |
SRA |
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| Source name |
seedling
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| Organism |
Oryza sativa |
| Characteristics |
tissue: seedling
antibody: anti-BG4
genotype: WT
treatment: K+PDS G4 stabilizing buffers
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| Growth protocol |
temperature of 28–30 °C and a 14 h/10 h light/dark cycle
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
collected and cut into small slices of 1–1.5 cm in size, followed by cross-linking with a 1% final concentration of formaldehyde for 10 min under vacuum.
DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing termed BG4-DNA-IP-seq. Briefly, 5 μg of fragmented genomic DNA was denatured and reassociated in the G4 stabilization buffer (40% PEG200, 10 mM Tris-HCl, pH 7.5, with 150 mM KCl or NaCl), which was then followed by incubation with anti-BG4-FLAG antibody in the IP incubation buffer (50 mM HEPES, 150 mM KCl, 1 mM MgCl2, 130 nM CaCl2, 1% BSA, 40% PEG200, Complete Mini, pH 7.5). After adding anti-FLAG antibody (D110005, BBI, Shanghai, China) and washed protein G Dynalbeads (10004D, Invitrogen, Carlsbad, CA, USA) for additional 4 h followed by washing two times, anti-BG4 recognized DNA-G4s was finally recovered for library preparation. IPed and input DNA was used for library preparation using the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina (E7645S, NEB). All libraries were sequenced on the Illumina platform.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequences using trim_galore
BWA (Burrows-Wheeler Aligner) with default parameters was used to align all cleaned reads to the MSU v7.0 reference genom
MACS was used to call IP-G4 (referred to as G4s pulled down by anti-BG4 antibody) peaks from reads with an alignment length greater than 50.
Assembly: MSU v7.0
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: BG4-DNA-IP-Seq
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| Submission date |
Jul 13, 2023 |
| Last update date |
Jan 17, 2024 |
| Contact name |
huang ran ran |
| E-mail(s) |
r17860736537@yeah.net
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| Organization name |
Nanjing Agricultural College
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| Street address |
weigang 1
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| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE237294 |
Epigenomic features and potential functions of PEG and PDS favorable DNA G-quadruplexes in rice |
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| Relations |
| BioSample |
SAMN36437665 |
| SRA |
SRX21011367 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7604305_K+PDS_rep1.bw |
72.6 Mb |
(ftp)(http) |
BW |
| GSM7604305_K+PDS_rep1.peaks.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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