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| Status |
Public on Apr 18, 2021 |
| Title |
Ardisia pusilla toluene treatment rep1 |
| Sample type |
SRA |
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| Source name |
Ardisia pusilla
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| Organism |
Ardisia pusilla |
| Characteristics |
tissue: leaves
size: 20 cm height
treatment: treated with 1.5ppm toluene for 5 hours
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| Treatment protocol |
A. pusilla plants (20 cm height) grown in a greenhouse were placed in a sealed chamber at room temperature (25±5 °C) under a pressure of 760 mm Hg with 12/12 h light/dark cycle. After that, toluene treatment was applied at a concentration of 1.5 ppm inside the chamber for 5 h. A. pusilla plants without toluene treatment were used as controls.
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| Growth protocol |
A. pusilla plants were kept in greenhouses.
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| Extracted molecule |
total RNA |
| Extraction protocol |
A. pusilla leaf samples were ground into powder in a mortar with liquid nitrogen, and total RNA was extracted from the samples using TRIzol reagent (MRC, Cincinnati, OH, USA).Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls performed using Sequencing Control Software
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed reads for every sample were merged into one file to construct combined reference. The de novo assembly of merged data was carried out using Trinity with default parameters; it can be assembled into transcript contigs.
For assembled genes, longest contigs of the assembled contigs are filtered and clustered into the non-redundant transcripts using CD-HIT-EST program. We defined these transcripts as ‘unigenes’ which are used for predicting the ORFs (Open Reading Frames), annotating against several known sequence databases, and analyzing differentially expressed genes (DEGs).
Genome_build: In this study, Other de novo transcriptome assembly was performed in order to reconstruct the transcript sequences without reference genome sequence. To annotate the clustered unigenes, they were blasted against public databases with a blastx and BLASTN and BLASTX, including Kyoto Encyclopedia of Genes and Genomes (KEGG), NCBI Nucleotide (NT), Pfam, Gene ontology (GO), NCBI non-redundant Protein (NR), UniProt and EggNOG.
Supplementary_files_format_and_content: WT and Toluene treated Excel files include FPKM values for each Sample.
Supplementary_files_format_and_content: merge_Annotation_Result file include raw gene counts for every unigene
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| Submission date |
Apr 17, 2021 |
| Last update date |
Apr 18, 2021 |
| Contact name |
Su Young Lee |
| E-mail(s) |
lsy8542224@korea.kr
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| Organization name |
Rural Development Administration
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| Department |
Floriculture Research Division, National Institute of Horticultural and Herbal Science
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| Street address |
100, Nongsaengmyeong-ro, Iseo-myeon
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| City |
Wanju-gun |
| State/province |
Jeollabuk-do |
| ZIP/Postal code |
55365 |
| Country |
South Korea |
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| Platform ID |
GPL30010 |
| Series (1) |
| GSE172268 |
Transcriptomic analysis for the identification of metabolic pathway genes related to toluene response in Ardisia pusilla |
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| Relations |
| BioSample |
SAMN18789107 |
| SRA |
SRX10627062 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5251158_Toluene_1.xlsx |
22.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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