|
| Status |
Public on Apr 03, 2015 |
| Title |
TAG5 Control BR2 |
| Sample type |
SRA |
| |
|
| Source name |
TAG5 Control BR
|
| Organism |
Eucalyptus grandis |
| Characteristics |
clonal genotype: TAG5
response to c. austroafricana infection: tolerant
inoculated with: C. austroafricana
time point: 3 days post inoculation
tissue: stem
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the stem material was extracted using the CTAB protocol and purified with a Qiagen Rneasy mini kit
Library construction was performed at BGI
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
processed data file: TAG5_Cuffdiff_gene_differential_expression_testing.txt
|
| Data processing |
Quality control of the raw reads was performed using FASTQXC
Reads were mapped to the E. grandis genome using Tophat v2.0.4
FPKM values were generated using Cufflinks v1.0.3
Differential gene expression was performed using Cuffdiff v1.0.3
Genome_build: Eucalyptus grandis v1.1; http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Egrandis
Supplementary_files_format_and_content: Tabular cuffdiff gene lists of differentially expressed genes between the controls and inoculated samples in each genotype
|
| |
|
| Submission date |
Apr 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronishree Mangwanda |
| E-mail(s) |
ronishree.mangwanda@fabi.up.ac.za
|
| Organization name |
University of Pretoria
|
| Street address |
Lynwood Road
|
| City |
Pretoria |
| ZIP/Postal code |
0001 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL19989 |
| Series (1) |
| GSE67554 |
Transcriptional profiling of Eucalyptus grandis challenged with Chrysoporthe austroafricana |
|
| Relations |
| BioSample |
SAMN03459100 |
| SRA |
SRX977823 |
