|
Status |
Public on May 19, 2020 |
Title |
C30 (Sample 22) |
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: 30 min biological replicate: 3
|
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.
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|
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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
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|
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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 |
SAMN14944664 |
SRA |
SRX8357855 |