|
| Status |
Public on Sep 26, 2023 |
| Title |
leaf,R-loop,CK_2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: leaf
genotype: S9.6
treatment: grow in the normal conditions
|
| Treatment protocol |
At the 13th day, a half of PCR plates with seedlings were continued to grow in the normal conditions (CK) and another half were grown at 4℃ for cold treatment. After a 24 h cold treatment (COLD), two biological replicates of CK and cold treated (COLD) seedlings were collected and stored at −80°C for later use.
|
| Growth protocol |
Seeds of Nipponbare (Oryzasativa ssp. japonica) were pre-germinated at room temperature under dark conditions for 3 days. Uniformly germinated seeds were individually put into 96-well PCR plates with bottom cut. Each plate with germinated seeds were put into the liquid culture medium for continuing to grow under a mean temperature as 28/22°C and 12 h/12 h for a light-dark cycle in the greenhouse.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Uniformly germinated seeds were individually put into 96-well PCR plates with bottom cut. Each plate with germinated seeds were put into the liquid culture medium for continuing to grow under a mean temperature as 28/22°C and 12 h/12 h for a light-dark cycle in the greenhouse.
Total RNA was extracted from CK and COLD seedlings, respectively, using the RNeasy plant Mini kit (Qiagen, 74904). After removal of genomic DNA contamination using DNase I treatment, approximately 30 µg total RNA was used for mRNA enrichment using oligo (dT) conjugated magnetic beads.The DNA-RNA hybrid immunoprecipitation (DRIP) experiment and DRIP-seq libraries were conducted as described before
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
DRIP-seq
|
| Data processing |
For RNA-seq analyses, the quality of raw reads was assessed using FastQC (Kroll et al. 2014). Raw reads were cleaned after removal of adapters and poor-quality bases using Trimmomatic (version 0.39) (Bolger et al. 2014). Clean reads were aligned to the rice reference genome using Hisat2 (version 2.1.0) (Kim et al. 2015). The number of reads mapped to each gene was counted using FeatureCounts (version 1.6.4) (Liao et al. 2014). FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values were calculated to represent the gene expression levels.
For DRIP-seq data analyses, the raw data were processed for removal of adapter and low-quality bases using TrimGalore (version0.4.3,Babraham Bioinformatics). Clean reads were aligned to the rice reference genome (MSU version7.0) using Bowtie (Langmead et al. 2009) with the following parameters‐‐best‐‐strata -m 1 - x 800. Additional duplicate reads were removed by using the SAMtools rmdup,version1.4 (Li et al. 2009). The strand-specific reads were separated using flags of SAM files. The direction of R-loops was determined according to the direction of the R2 reads (R1 for the paired-end reads) aligned to the genome.
Assembly: MSU v7.0
|
| |
|
| Submission date |
Aug 21, 2023 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Zexue He |
| E-mail(s) |
hezexue@stu.njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Department |
Agricultural College
|
| Street address |
Xuanwu District,1 Weigang
|
| City |
Nanjing |
| State/province |
Jiangsu Province |
| ZIP/Postal code |
210018 |
| Country |
China |
| |
|
| Platform ID |
GPL23876 |
| Series (1) |
| GSE217841 |
R-loops act as a master regulatory switch modulating transcription of cold-responsive genes in rice |
|
| Relations |
| BioSample |
SAMN37101213 |
| SRA |
SRX21445799 |
