|
| Status |
Public on May 19, 2020 |
| Title |
C180 (Sample 8) |
| Sample type |
SRA |
| |
|
| Source name |
B. rapa leaf
|
| Organism |
Brassica rapa |
| Characteristics |
genotype: Wild type
tissue: 1st true leaf
treatment: chitin (100µg/mL)
treatment time: 180 min
biological replicate: 1
|
| Treatment protocol |
Water or water solution of flg22 (100nM) or chitin (100µg/mL) for 30 or 180 min
|
| Growth protocol |
B. rapa plants were grown on soil in a short day condition (10h-light, 14h-dark) for 17 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the leaf tissue using Accuzol total RNA extraction reagent (Bioneer) according to the manufacturer's instructions
1µg of total RNA was used for RNA-seq library preparation for each sample. RNA-seq libraries were prepared with TruSeq Stranded mRNA LT Sample Prep kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were quality trimmed and filtered using Trimmomatic v0.36
Reads were aligned to Brassica rapa reference genome v1.5 (http://brassicadb.org/brad/datasets/pub/BrassicaceaeGenome/Brassica_rapa/V1.0/Bra_Chromosome_V1.5/) using HISAT2
Transcripts were assembled, read counts and FPKM values were calculated using StringTie v2.0
DEG (Differentially Expressed Genes) analysis was performed with DESeq2
Genome_build: http://brassicadb.org/brad/datasets/pub/BrassicaceaeGenome/Brassica_rapa/V1.0/Bra_Chromosome_V1.5/Brapa_sequence_v1.5.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample as defined by Stringtie, excel table file summarizing the foldchange of DEG in different treatments realtive to corresponding water treatments
|
| |
|
| Submission date |
May 18, 2020 |
| Last update date |
May 19, 2020 |
| Contact name |
Cecile Segonzac |
| E-mail(s) |
csegonzac@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Department |
Department of Plant Science
|
| Lab |
Horticultural Crop Molecular Physiology Lab
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL28300 |
| Series (1) |
| GSE150746 |
Transcriptome profiling of Brassica rapa subsp. pekinensis treated with immunity elicitors |
|
| Relations |
| BioSample |
SAMN14944678 |
| SRA |
SRX8357841 |
