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Status |
Public on Jul 26, 2023 |
Title |
alkbh1-6mA-1 |
Sample type |
SRA |
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Source name |
seedling
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Organism |
Oryza sativa Japonica Group |
Characteristics |
tissue: seedling genotype: ALKBH1 knockout chip antibody: Anti-6mA(SYSY,#202-003)
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Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted using DNeasy plant mini kit (QIAGEN, Germany) according to the manufacturer’s instructions. ChIP DNA libraries were prepared using a TruSeq DNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA)
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
RNA-Seq The RNA-seq clean data were mapped against the MSU version 7.0 rice genome with the corresponding annotation by hisat2 using default parameters FeatureCounts (v2.0.0)and DESeq2 (v1.26.0)were used to calculate DEGs. ChIP-Seq the adaptors were trimmed from the raw reads with Trimmomatic version 0.36 (Bolger et al., 2014) with the arguments: ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15. The ChIP clean reads were mapped to the MSU7.0 genome with Bowtie2 (version 2.4.2) using default parameters. Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01 The DESeq2 method implemented in DiffBind was used to test the differential peak Assembly: MSU version 7.0 rice genome Supplementary files format and content: tab-delimited text file include counts for each Sample Supplementary files format and content: bigWig, broadPeak,narrowPeak (except for Input sample) Library strategy: 6mA-seq
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Submission date |
Jan 12, 2023 |
Last update date |
Jul 26, 2023 |
Contact name |
Qingxiao Jia |
Organization name |
HZAU
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Lab |
National Key Laboratory of Crop Genetic Improvement
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Street address |
No.1,Shizishan Street
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City |
Wuhan |
State/province |
Hubei |
ZIP/Postal code |
430000 |
Country |
China |
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Platform ID |
GPL18525 |
Series (1) |
GSE222734 |
A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature |
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Relations |
BioSample |
SAMN32709856 |
SRA |
SRX19015306 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6929623_alkbh1-6mA-1.bw |
36.0 Mb |
(ftp)(http) |
BW |
GSM6929623_alkbh1-6mA-1.narrowPeak.gz |
757.7 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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