 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 31, 2016 |
| Title |
hot_replicate_2 |
| Sample type |
SRA |
| |
|
| Source name |
National Institute of Agricultural Research, Japan
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: germinating seeds
developmental stage: 5 days after germination
cultivar: Kasalath
|
| Growth protocol |
A total of 40 Kasalath seeds were used; 5 Kasalath seeds were placed in damp tissue with no media, in labelled petri dishes. 4 petri dishes were placed in the lab at 25 °C and were covered with a small cardboard box and the 4 petri dishes were placed in the Binder Cooled Incubator (Model KB23) where the temperature was set at 35°C and remained constant throughout the experiment. Tissues in petri dishes were dampened with tap water until the 8th day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The mirVana™ miRNA Isolation Kit was used to extract the total RNA and isolate the sRNA from germinating seeds
Libraries were constructed using the NEBNext® Small RNA Library Prep Set for Illumina® kit according to the manufacturer's instructions. Size selection was performed using AMPure XP Beads (E7330)
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
isolated sRNA
S3
|
| Data processing |
Base calling was performed by the Illumina Real Time Analysis (RTA) 1.18.54 software launched by the Miseq Control Software (2.4.1.3). Raw fastq reads were imported into the UEA sRNA workbench 3.2 and trimmed for adaptor sequences followed by filtering of low complexity sequences, sequences below 8nt, sequences above 35nt, sequences that match known transfer RNAs and sequences that match known ribosomal RNAs. The miRProf tool was used to align the filtered sequences to the mirBase 21 dataset of mature miRNAs in the plant category. Parameters were set to allow 0 mismatches, disallow overhangs, keep only best matches, disallow grouping variants, organisms, mature and star sequences. Normalised expression values were calculated by multiplying the raw number of reads matching an miRNA by a million divided by the total number of filtered reads in the sample. The rice miRNAs predicted targets and the description of the targets were found using the web software psRNAtarget and accessed through this web address (http://plantgrn.noble.org/psRNATarget/). miRNA sequences in fasta format were uploaded and Oryza Sativa (rice), transcript, MSU Rice Genome Annotation, version 7 was selected for target search. Other parameters were maximum expection (3.0); Length of complementarity scoring (hspsize) (20); # of top target genes for each small RNA (200); Target accessibility - allowed maximum energy to unpair the target site (UPE)( 25.0) ;Flanking length around target site for target accessibility analysis (17 bp in upstream / 13 bp in downstream);Range of central mismatch leading to translational inhibition (9 - 11 nt). Genome Build: miRBase 21. Supplementary_files_format_and_content: abundance
|
| |
|
| Submission date |
Aug 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Huan You Gan |
| Organization name |
Monash University Malaysia
|
| Street address |
Jalan Lagoon Selatan
|
| City |
Bandar Sunway |
| State/province |
Selangor |
| ZIP/Postal code |
47500 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL20819 |
| Series (1) |
| GSE72160 |
Small RNAs in rice cultivar Kasalath (Oryza sativa L.) induced by high temperatures during germination |
|
| Relations |
| BioSample |
SAMN03998622 |
| SRA |
SRX1156671 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
