|
| Status |
Public on Jun 14, 2017 |
| Title |
lower leaf - plant 3 |
| Sample type |
SRA |
| |
|
| Source name |
leaf, severe C. zeina infection
|
| Organisms |
Zea mays; Cercospora zeina |
| Characteristics |
maize cultivar: B73
tissue: lower leaf
c. zeina infection: severe
plant id: 3
|
| Growth protocol |
Maize B73 grown in the field in Greytown, Kwazulu-Natal, South Africa with natural infection of Cercospora zeina. Planted in December 2012.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiazol, treated with DNase, and purified with RNeasy Plant Mini kit according to manufacturer's instructions (Qiagen, Hilden, Germany). Total RNA was shown to be of good quality using an Agilent Bioanalyser (average RIN number = 7.7).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
BR3B
Maize leaf with severe infection by C. zeina.
Processed data file: edgeR_BR_all.txt
|
| Data processing |
Data were filtered to remove adapters and trimmed for quality using
Trimmomatic (v0.30; (Bolger et al., 2014); settings
TruSeq3-PE-2.fa:2:30:10 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Filtered reads were aligned to a combined Zea mays genome (v5b.60 from the Phytozome v9.1 resource, Schaeffer et al., 2013) and the draft genome of Cercospora zeina (GenBank SUB212877) using Tophat2 with following setting: -p 4 -r 0 --mate-std-dev 200.
The longest transcript gene structure in the Z. mays annotation GFF3 file (retrieved from the Phytozome v9.1 resource) was used to estimate the transcript abundance in each locus by HTSeq.
Final data output include only values for Cercospora zeina genes.
Genome_build: Cercospora zeina draft genome
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each gene.
|
| |
|
| Submission date |
Feb 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dave Kenneth Berger |
| E-mail(s) |
dave.berger@up.ac.za
|
| Phone |
+27124204634
|
| Organization name |
University of Pretoria
|
| Department |
Plant and Soil Science
|
| Lab |
Molecular and Plant Pathogen Interactions
|
| Street address |
Lynnwood Road
|
| City |
Pretoria |
| State/province |
Gauteng |
| ZIP/Postal code |
0002 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL23023 |
| Series (1) |
| GSE94442 |
Maize and Cercospora zeina transcriptome analysis during gray leaf spot foliar disease |
|
| Relations |
| BioSample |
SAMN06291431 |
| SRA |
SRX2534914 |
