 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 18, 2018 |
| Title |
tomato degradome 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole tissue
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: whole tissue
cultivar: Heinz
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from whole tissue of pepper, tomato and potato using Ambion™ TRIzol™ Reagent, according to the manufacturer's protocol.
Degradome libraries were constructed as previously described (Addo-Quaye et al., Current Biology, 2008).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
two technical replicates
|
| Data processing |
Adaptors were removed and the qualified reads in size 15-26 nucleotides were obtained.
Structural RNAs such as rRNAs, tRNAs, snRNAs and snoRNAs were removed using BLASTN against Rfam.
Repeats and transposons were also removed using the repeat database.
The remaining reads were mapped to transcript sequences by Bowtie.
Because UTR sequences have not been identified in pepper, tomato and potato, transcripts were defined to coding sequence and ±1kb flanking sequences.
Target genes of microRNAs were identified by CleaveLand4 pipeline (cutoff: p-value ≤ 0.05 or score ≤ 4)
Genome_build: Pepper.v.1.55, ITAG v.2.3, JGI v.4.03
Supplementary_files_format_and_content: counts/# reads
|
| |
|
| Submission date |
Aug 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chanseok Shin |
| E-mail(s) |
cshin@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Department |
Agricultural Biotechnology
|
| Lab |
Biochemistry
|
| Street address |
1, Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE102781 |
Genome-wide comparative analysis in Solanaceae plants reveals evolution of novel miRNAs targeting defense genes in Capsicum spp. |
|
| Relations |
| BioSample |
SAMN07514839 |
| SRA |
SRX3101061 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
