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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 26, 2023 |
| Title |
alkbh1-6mA-Input |
| 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: none
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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 |
SAMN32709854 |
| SRA |
SRX19015308 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6929625_alkbh1-6mA-Input.bw |
39.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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