|
| Status |
Public on Aug 07, 2023 |
| Title |
hst_sc_pU |
| Sample type |
SRA |
| |
|
| Source name |
sperm cells
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: sperm cells
genotype: hst-6
treatment: small RNA pseudouridine IP (hst-6)
|
| 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 small RNA studies, adapters were removed (cutadapt),PCR duplciates were removed (prinseq-lite), reads were trimmed and size selected (cutadapt). Reads corresponding to miRNAs were selected using ‘mirnasoft’ package and counted, number of reads corresponding to TE-siRNA were obtained using bedtools package. Analysis was performed using 'DESeq2'
BED file
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 |
SAMN32534645 |
| SRA |
SRX18906653 |
