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| Status |
Public on Jun 12, 2024 |
| Title |
Col-0-2 |
| Sample type |
SRA |
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| Source name |
Whole plants
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Whole plants
ecotype: Col-0
genotype: wildtype
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using the RNeasy Plant Mini Kit (QIAGEN, Valencia, CA) and treated with DNase I (NEB, USA).
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
replicate 2
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| Data processing |
Quality of raw reads were pre-checked using the FastQC software.
Trimmed reads of each sample were aligned to the Arabidopsis TAIR10 genome using STAR aligner with default parameters.
Mapped reads were converted to digital counts using FeatureCounts and were analyzed using edgeR.
DEGs were identified based on an adjusted p-value <0.05 and an absolute log2 fold change ≥ 1.
Assembly: Arabidopsis thaliana reference genome (TAIR10) was downloaded via the TAIR database (https://www.arabidopsis.org/)
Supplementary files format and content: bw files for individual samples
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| Submission date |
Dec 18, 2023 |
| Last update date |
Jun 12, 2024 |
| Contact name |
Dasom Choi |
| E-mail(s) |
somich429@gmail.com
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| Organization name |
Chung-Ang University
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| Street address |
4726, Seodong-daero
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| City |
Anseong-si |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
17546 |
| Country |
South Korea |
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| Platform ID |
GPL26208 |
| Series (1) |
| GSE250418 |
A light signaling factor, ELONGATED HYPOCOTYL 5 (HY5) interacts with Histone deacetylase 9 (HDA9) to play a suppressive role in the glucosinolate biosynthesis in Arabidopsis |
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| Relations |
| BioSample |
SAMN38881112 |
| SRA |
SRX22919644 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7978888_Col_2.bw |
16.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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