|
| Status |
Public on Oct 01, 2019 |
| Title |
DCL_1 (small RNA) |
| Sample type |
SRA |
| |
|
| Source name |
TBSV incubated cells
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: BY2
lysate: BY2 lysate (BYL)
treatment: exposed TBSV dsRNA to the BYL
sequencing input: RNA of TBSV dsRNA-incubated extract
|
| Treatment protocol |
BY-2 protoplasts were generated by treatment with Cellulase RS and Pectolyase Y-23. Evacuolated BY-2 protoplasts were obtained by percoll gradient centrifugation and extracts (BYL) were prepared by disrupting cells using a dounce homogenizer.
|
| Growth protocol |
Nicotiana tabacum BY-2 cells were grown in Murashige-Skoog liquid medium at 23°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from DCL assays or AGO/RISC immunoprecipitations by treatment with proteinase K followed by Phenol/Chloroform extraction and ethanol precipitation
RNA libraries were prepared using illumina protocolls.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
JS_21
|
| Data processing |
adapter trimming by cutadapt
quality filtering by sickle -q 20 -l 15
mapping by bowtie-1.1.2 (-n 3 --best --strata) to combined reference of the tobacco genome (Ntab-BX_AWOK-SS.fa) and the TBSV sequence (TBSV.fa)
sambamba -view -f TBSV
input of mapped reads by Rsamtools
mapped reads were partitioned into six sets depending on the read-lengths (21, 22, or 24 nucleotides) and the mapped strand (positive or negative), and the starting positions of the mapped reads were counted as peak expression
Reads were stored in 5’ to 3’ orientation in the Sequence Alignment Map (SAM) format, so the first (last) nucleotide was counted for reads mapped onto the positive (negative) strand
Genome_build: Ntab-BX_AWOK-SS.fa (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/sierro_et_al_2014/assembly/Ntab-BX_AWOK-SS.fa.gz) + TBSV.fa
Supplementary_files_format_and_content: semicolon-delimited text files include raw peak counts for each Sample.
|
| |
|
| Submission date |
Oct 23, 2018 |
| Last update date |
Oct 01, 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) |
| GSE121644 |
Highly efficacious antiviral protection of plants by siRNAs identified in vitro |
|
| Relations |
| BioSample |
SAMN10275092 |
| SRA |
SRX4917215 |
