|
| Status |
Public on Nov 24, 2012 |
| Title |
control |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Saccharum hybrid cultivar SP70-1143 |
| Characteristics |
genotype: SP70-1143
treatment: control
tissue: leaf
|
| Treatment protocol |
After the acclimation period, salinity stress was induced with a concentration of 170mM (mild) in plantlets by adding the salt to the Hoagland solution. The time-course established was (0, 1, 6 and 24hs). For each time point, a group of three plants was submitted to stress, and other three plants used as controls. Individual plants were used for the analysis. All experiments were carried in a greenhouse at 28ºC, 16 hours/light and 8 hours/dark.
|
| Growth protocol |
Saccharum sp Cv. SP70-1143 plantlets were grown in vitro for approximately 1 month in Murashige and Skoog media supplemented with kinetin (0,1mg/ml), Indol butyric acid (I-BA- 0,2mg/ml) and citric acid (150mg/ml). Next, these plantlets were transferred to a hydroponic system supplied with 1x Hoagland’s solution and grown for 2 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from whole plants using Trizol (Invitrogen, CA, USA) as described by the manufacturer.
TruSeq Small RNA Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Quality of the sequences was evaluated by measuring the quality of the reads according to the percentage of bases having a base quality greater or equal than 30 (Q30)
3’ Illumina adapters (CTGTAGGCACCATCAAT) and “N” bases were trimmed
Using the UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) and three different databases - all plant t/rRNAs from Rfam, all Arabidopsis tRNAs from The Genomic tRNA Database and all plant t/rRNA sequences from EMBL release - reads with low-complexity (less than 3 different bases) and both sense and antisense matches with t/rRNAs were removed
Detection of conserved miRNAs with UEA sRNA toolkit-Plant version miRProf pipeline was done allowing three mismatches with mature miRNAs from miRBase (v17.0). Only reads with match to Sorghum bicolor were included in the analysis.
The output of the miRProf contains information about unique sequences counts. Counts were normalized in reads per 1 million (RPM) and total reads counts after the final trimming and filtering steps were used for normalization
Genome_build: Sorghum bicolor v1.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample
|
| |
|
| Submission date |
Nov 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Paulo Ferreira |
| E-mail(s) |
paulof@bioqmed.ufrj.br
|
| Organization name |
Universidade Federal do Rio de Janeiro
|
| Street address |
Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária
|
| City |
Rio de Janeiro |
| ZIP/Postal code |
21941-590 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL16317 |
| Series (1) |
| GSE42484 |
High-throughput sequencing of small RNA transcriptome reveals salt stressed regulated microRNAs in sugarcane |
|
| Relations |
| SRA |
SRX206186 |
| BioSample |
SAMN01818647 |
