|
| Status |
Public on Aug 07, 2023 |
| Title |
WT_pollen_CMC+_Mn_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pollen
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: pollen
genotype: WT
treatment: RNA treated with CMC, RT performed using Mn ions
|
| Growth protocol |
temp 22C, long day, 14 days old seedlings were grown on ½ MS plates, older plants were grown on soil
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NEXTFLEX Small RNA-seq v3 Kit (PerkinElmer)
RNA was extracted with Trizol and using the Direct-zol kit (Zymo Research)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
For miRNA mismatch analysis, adapters sequences were removed and reads were trimmed (cutadapt). Reads were aligned to the genome using BWA and processed with SAMtools. Final files were obtained using ‘bam-readcount’ and AWK scripts
txt file containing mapping information for each position in the miRNA sequence
Assembly: tair10
|
| |
|
| Submission date |
Jan 12, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Jakub Jacek Dolata |
| E-mail(s) |
j.dolata@amu.edu.pl
|
| Organization name |
Adam Mickiewicz University
|
| Department |
Department of Gene Expression
|
| Street address |
Uniwersytetu Poznanskiego 6
|
| City |
Poznan |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN32532917 |
| SRA |
SRX18904996 |
