|
| Status |
Public on Aug 03, 2020 |
| Title |
0D_10-3_1_miRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis ecotype Columbia (Col-0)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: Sound wave (10KHz)
ecotype: Columbia (Col-0)
drenched pathogen: Ralstonia solanacearum
time after pathogen drench: 0d
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the mirVana miRNA isolation kit (Ambion).
Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
After TruSeq small RNA adapters were eliminated among the sequenced reads by Trimommatic software (v.0.33), the remained sequence data were mapped to the Arabidopsis genome (TAIR10) using bowtie2 (v.2.2.2).
The quantification of each miRNA was estimated using HTSeq software package.
The read counts per
million fragments mapped (CPM) of each sample were used to estimate the expression level of each gene. The CPM data were normalized by the quantile method and log2 transformation.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text format with CPM values of miRNA
|
| |
|
| Submission date |
Jun 26, 2019 |
| Last update date |
Aug 03, 2020 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
|
| Phone |
+82-42-879-8107
|
| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE133321 |
Expression profiling by small RNA-seq for identifying miRNA associated with sound vibration in plant |
| GSE133325 |
Identifying genes associated with sound vibration in plant |
|
| Relations |
| BioSample |
SAMN12139234 |
| SRA |
SRX6367433 |
