 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 26, 2023 |
| Title |
OEALKBH1-RNA-seq-2 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: seedling
genotype: ALKBH1 overexpression
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
RNA-seq library construction using the TruSeq RNA Library Preparation Kit (Illumina, USA), according to the manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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)
|
| |
|
| Submission date |
Jan 12, 2023 |
| Last update date |
Jul 26, 2023 |
| Contact name |
Qingxiao Jia |
| Organization name |
HZAU
|
| Lab |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
No.1,Shizishan Street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430000 |
| Country |
China |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE222734 |
A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature |
|
| Relations |
| BioSample |
SAMN32709864 |
| SRA |
SRX19015298 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
