|
| Status |
Public on Nov 23, 2024 |
| Title |
CK_BS-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Control (CK)
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
tissue: Leaves
treatment: ordinary hydroponic treatment
tissue: rice seedlings
age: two-week-old rice seedlings
|
| Treatment protocol |
The sterilized rice seeds were seeded in 1/2 MS medium containing 0.56 mg/ml CDs. We used 1/2 MS as control. The seeds were grown in an artificial climate chest for three weeks.
|
| Growth protocol |
For seedling growth, shelled rice seeds (Nipponbare, Oryza. sativa L. Japonica) were sterilized in 2% sodium hypochlorite containing 0.1% tween-20 for 15 min, followed by three times of washing using pure water.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For germination assay, rice seeds were soaked in pure water containing different concentrations of CDs for 48 h, then cultured in room temperature for another two days. The length of seminal root was statistically analyzed.
mRNA-seq libraries were prepared and sequenced on Illumina NovaSeq platform.
The BS-treated DNA was finally PCR-amplified and sequenced in paired-end 150 bp mode on Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Methylation (5mc)
|
| Data processing |
[RNA-seq] The raw sequence data were processed using FastQC (v0.11.5) and fastp (v0.21.0) (--length_required=50) for removing low-quality reads. The filtered high-quality paired-end reads were aligned to the rice reference genome with MSU version 7.0 (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) using HISAT2 (v2.0.5) with default parameters.
[RNA-seq] The cleaned reads were then aligned to the rice reference genome (MSU version 7.0) (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) using Bismark program (v0.23.0) (--bowtie2 -p 20 -N 0 -L 20), Reads with a mapping quality below twenty were excluded from further analyses using SAMtools (v1.9) (-q 20). FeatureCounts (v1.6.4) (-g gene_id) was used to obtain read counts for all annotated genes in the rice reference genome.
[RNA-seq] To compare expression levels across samples and genes, the RNA-seq read density of each gene was normalized based on the gene length and the sequencing depth [i.e., transcripts per million (TPM)].
[BS-seq] For data analyses, paired-end sequencing reads were first trimmed with fastp (v0.21.0) (--length_required=50) for removal of adapters and low-quality reads. The cleaned reads were then aligned to the rice reference genome (MSU version 7.0) (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) using Bismark program (v0.23.0) (--bowtie2 -p 20 -N 0 -L 20)
[BS-seq] PCR duplicates were removed using the deduplicate_bismark implemented in the Bismark program.
[BS-seq] The extent of the cytosine methylation was determined using the bismark_methylation_extractor implemented in the Bismark program.
Genome_build: Genome_build: http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/
Supplementary_files_format_and_content: [RNA-seq] tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: [RNA-seq] Matrix table with raw read counts for every gene and every sample
Supplementary_files_format_and_content: [RNA-seq] bigwig
Supplementary_files_format_and_content: [BS-seq] bigwig; gz for the extent of the cytosine methylation
|
| |
|
| Submission date |
Nov 23, 2021 |
| Last update date |
Nov 23, 2024 |
| Contact name |
zhenyu luo |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing Agricultural University
|
| Department |
College of Agricuture
|
| Lab |
Zhanglab
|
| Street address |
Xuanwu
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE189428 |
Epigenetic characterization of carbon dots functions in rice |
|
| Relations |
| BioSample |
SAMN23411051 |
| SRA |
SRX13209631 |
