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Experiment information
Accession CRX263600
Organism Arabidopsis thaliana
Title DRIP_replicate_1
BioProject PRJCA005944
BioSample SAMC439846
Platform Illumina HiSeq X Ten
Library
Library name Construction protocol Strategy Source Selection Layout
Nuclei were isolated from Arabidopsis plants, followed by SDS/proteinase K treatment at 37 overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, NlaIII, DdeI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55. DNA was purified and sonoicated to 150 bp fragments .The first adapter was ligated to the 3' end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3' ends of ssDNA and ligates the first truncated adapter to 3' ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5' ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified. OTHER GENOMIC PCR PAIRED
Processing Planned read length (bp) for mate 1: 150
Planned read length (bp) for mate 2: 150
Release date2024-04-16
Run
Run accession Run data file information
File nameFile size (MB)
CRR309674 CRR309674_f1.fastq.gz
CRR309674_r2.fastq.gz
5,980.07
6,515.58
SubmitterZhi John Lu (lulab1@mail.tsinghua.edu.cn)
OrganizationTSINGHUA UNIVERSITY
Date submitted2021-08-06