 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 01, 2013 |
| Title |
35S>>SlDCL1IR-2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings shoots
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: M82
genotype/variation: SlDCL1 silenced (35S>>SlDCL1IR)
age: 14 days after sowing
tissue: seedling shoots
|
| Growth protocol |
growth chamber with a 16 h light period and 8 h dark period 24 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tri-reagent extraction
Total RNA samples were used to construct small RNA libraries using the TruSeq small RNA kit as described by the manufacturer (Illumina, San Diego, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 4
|
| Data processing |
The Cache ASsisted Hash Search with Xor logic (CASHX) Pipeline (release 2.3) was used to parse and map the small sequences to the tomato genome SGN release version SL2.40
Reads in the size range of 18-26 nts and perfectly matched to the tomato genome were retained.
The small RNA CASHX database was annotated with the Repeats Master version 5.0 (ftp://ftp.solgenomics.net/tomato_genome/repeats/), Plant snoRNAs Database (version 1.2; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home), SILVA rRNA database (http://www.arb-silva.de/), miRbase (release 19)http://www.mirbase.org/);
After annotation, only "clean" reads not matching tRNAs, rRNAs, snRNA and SnoRNA were used for further analysis.
Genome_build: tomato genome (SGN release version SL2.40; http://solgenomics.net/organism/Solanum_lycopersicum/genome)
Supplementary_files_format_and_content: tab delimited values (txt) files include RPM values for each Sample
|
| |
|
| Submission date |
Oct 31, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Tzahi Arazi |
| E-mail(s) |
tarazi@agri.gov.il
|
| Phone |
972-3-9683498
|
| Organization name |
ARO - Volcani Center
|
| Department |
Institute of Plant Sciences
|
| Lab |
Tzahi Arazi
|
| Street address |
Institute of Plant Sciences, ARO the Volcani Center
|
| City |
Bet Dagan |
| State/province |
ISRAEL |
| ZIP/Postal code |
50250 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE51959 |
Global and local perturbation of the tomato microRNA pathway by a trans-activated DICER-LIKE 1 mutant |
|
| Relations |
| BioSample |
SAMN02389698 |
| SRA |
SRX372012 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1255898_35S_SlDCL1IR_2.txt.gz |
8.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
