|
| Status |
Public on Jun 22, 2024 |
| Title |
blade，accrual，30d，rep1 input |
| Sample type |
SRA |
| |
|
| Source name |
blade
|
| Organism |
Raphanus sativus |
| Characteristics |
tissue: blade
genotype: diploid
|
| Treatment protocol |
No processing has taken place
|
| Growth protocol |
The radish material used in this experiment was XHT, cultivated under the following conditions: daytime temperature of 25°C and 16 hours of light, and nighttime temperature of 23°C and complete darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaves were collected at 30 and 120 days after sowing, immediately stored in prepared tin foil, immediately immersed in liquid nitrogen for rapid cooling, and then transferred to a freezer at -80°C for long-term storage. For each library, leaves collected from three plants were mixed together and three independent biological replicates were performed for each sample.
RNA libraries for RNA-seq and m6A-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
XHT_F VS XHT_VG_Gene_differential_expression.txt
|
| Data processing |
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/). Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome raphanus sativus (Version: NA). Peak calling and diff peak analysis were performed by R package exomePeak (https://www.bioconductor.org/packages/3.3/bioc/html/exomePeak.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). HOMER (http://homer.ucsd.edu/homer/motif) was used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: Index of /download_genome/Brassica_Genome_data/Rapsa_Xiang_V1.0
Supplementary files format and content: txt and gz
|
| |
|
| Submission date |
Jun 20, 2024 |
| Last update date |
Jun 22, 2024 |
| Contact name |
wu lin jun |
| E-mail(s) |
lujb618@gmail.com
|
| Phone |
18848585509
|
| Organization name |
guizhou university
|
| Street address |
Xibei Street
|
| City |
Guiyang |
| State/province |
Guizhou |
| ZIP/Postal code |
550025 |
| Country |
China |
| |
|
| Platform ID |
GPL30556 |
| Series (1) |
| GSE270351 |
The Molecular Mechanisms of m6A Methylation Modification in Regulating Bolting and Flowering in Radish |
|
| Relations |
| SRA |
SRX24989583 |
| BioSample |
SAMN41935778 |
