|
| Status |
Public on Mar 06, 2016 |
| Title |
Root Control 30 rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Root_control_30_min
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbare
tissue: Root
age: 15 days old
time point: 30 minutes
|
| Treatment protocol |
Plants were treated with Margaporthe oryzae elicitors for 30 min and 2 hours
|
| Growth protocol |
Rice plants were grown for 2 week at 28ºC ans 16h/8h light/dark conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted with Trizol (Invitrogen) following manufacturer's instructions
TruSeq protocol (Illumina)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Small RNA
|
| Data processing |
Q20 Quality triming
Adaptor trimming
Size trimming (<18)
Read alignment to rice genome (using Bowtie2 aligner)
Reads aligning with Rfam v11.0 were removed
Read alignment to miRNA database (miRBase v21)
Total read library normalization
Genome_build: Oryza sativa, version 7.0
Supplementary_files_format_and_content: text file with reads and abundances for each detected miRNA
|
| |
|
| Submission date |
Mar 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Patricia Baldrich Gonzalez |
| E-mail(s) |
pbaldrich@ucdavis.edu
|
| Organization name |
University of California - Davis
|
| Department |
Meyers Lab
|
| Lab |
Meyers Lab
|
| Street address |
451 Health Sciences Dr., Davis, CA 95616
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL13160 |
| Series (2) |
| GSE66609 |
MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors [miRNA-Seq] |
| GSE66611 |
MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors |
|
| Relations |
| BioSample |
SAMN03392629 |
| SRA |
SRX905726 |
