|
| Status |
Public on May 09, 2018 |
| Title |
p19_1 |
| Sample type |
SRA |
| |
|
| Source name |
p19-pull down (p19 siRNA Binding Protein (NEB))
|
| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: BY2 lysate (BYL)
cultivar: bright yellow 2 (BY2)
|
| Growth protocol |
Nicotiana tabacum BY2 cells were grown in Murashige-Skoog liquid medium at 23°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Evacuolated BY2 protoplasts were obtained by percoll gradient centrifugation and extracts were prepared from cells disrupted by a dounce homogenizer. Small RNAs were precipitated by the p19 siRNA binding protein.
RNA libraries were prepared using illumina protocolls.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
adapter trimming by cutadapt
quality filtering by sickle -q 20 -l 15
maping by bowtie-1.1.2 to rRNA.fa
mapping of unmapped reads by bowtie-1.1.2 to HAIRPIN_SNORNA.fa
counting of mapped reads by Rsamtools
testing for differenial expression and normalisation by edgeR
Genome_build: miRBase v21
Supplementary_files_format_and_content: tab-delimited text files include raw counts and tmm normalized counts for each Sample.
|
| |
|
| Submission date |
May 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Claus Weinholdt |
| E-mail(s) |
claus.weinholdt@informatik.uni-halle.de
|
| Organization name |
Martin Luther University Halle-Wittenberg
|
| Department |
Institute of Computer Science
|
| Street address |
Von-Seckendorff-Platz 1
|
| City |
Halle |
| ZIP/Postal code |
06120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23484 |
| Series (1) |
| GSE98956 |
RNA sequencing of plant microRNAs precipitated by the tombusviral suppressor of RNA silencing p19. |
|
| Relations |
| BioSample |
SAMN07127013 |
| SRA |
SRX2828631 |
