|
| Status |
Public on Sep 21, 2020 |
| Title |
smallRNA_Col0_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
aerial tussue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col-0
genotype/variation: wild-type (WT)
|
| Growth protocol |
Plants were grown in soil under 16 hour light/8 hour dark cycle at 22°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Aerial parts of 4 weeks plants were collected and immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Direct-zol kit (Zymo Research) according to manufacturers instructions. Total RNA integrity was analyzed on Agilent 2100 Bioanalyzer. 10ug of RNA was resolved on denaturing 15%PAA gel and small RNA fraction was cout out from the gel
Libraries were constructed using the TruSeq SmallRNA Library Preparation Kit (Illumina) as described in the manual.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The adapter sequence was removed from the obtained raw reads with FASTX-Toolkit
Clean reads were mapped to all mature A. thaliana miRNAs from miRBase (release 22) using script countreads_mirna.pl (Eminaga et al., 2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: count reads, txt
|
| |
|
| Submission date |
Nov 14, 2018 |
| Last update date |
Sep 21, 2020 |
| Contact name |
Zofia Szweykowska-Kulinska |
| E-mail(s) |
zofszwey@amu.edu.pl
|
| Organization name |
Adam Mickiewicz University in Poznan
|
| Department |
Departemnt of Gene Expression
|
| Street address |
Umultowska 89
|
| City |
Poznan |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21785 |
| Series (2) |
| GSE122526 |
mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana [smallRNAs] |
| GSE122528 |
mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN10422822 |
| SRA |
SRX5007200 |
