|
| Status |
Public on Feb 14, 2020 |
| Title |
B10.R1.B: lower leaf - plant 1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf, moderate C. zeina infection (<4% GLS lesion area on leaves)
|
| Organism |
Zea mays |
| Characteristics |
maize cultivar: B73-QTL
tissue: lower leaf
c. zeina infection: severe
plant id: 1
|
| 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 |
B10.R1.B
|
| Data processing |
Reads 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 HEADCROP:15 SLIDINGWINDOW:4:20 MINLEN:50
Filtered reads were de novo assembled using Trinity (v2.5.1; (Haas et al., 2013) with default settings but Kmer=31 to create a "master assembly" of all reads from the six samples (3 lower leaf and 3 upper leaf)
The transcript abundance was estimated using salmon by mapping the filtered reads from each of the six samples to the "master assembly"
Differential expression analysis was done using edgeR
Annotation of the master assembly transcripts was done using PLAZA 4.0 workbench (maize B73 V4; B73-like and plant genes annotated by BLASTX against the plant genome within PLAZA)(C. zeina genes annotated based on the draft genome Genbank accession MVDW01000014.1)
Genome_build: maize B73 v4, Cercospora zeina draft genome (Genbank accession MVDW01000014.1)
Supplementary_files_format_and_content: Tab-delimited text file including log fold change for each gene.
|
| |
|
| Submission date |
Sep 10, 2019 |
| Last update date |
Feb 14, 2020 |
| Contact name |
Dave Kenneth Berger |
| E-mail(s) |
dave.berger@up.ac.za
|
| Organization name |
University of Pretoria
|
| Department |
Dept. Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI)
|
| Lab |
MPPI
|
| Street address |
Plant Sciences Complex, Entrance 11 - Corner Lunnon Road & Herold Street
|
| City |
Hatfield |
| State/province |
Gauteng |
| ZIP/Postal code |
0083 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL15463 |
| Series (1) |
| GSE137198 |
Maize and Cercospora zeina transcriptome analysis during gray leaf spot foliar disease |
|
| Relations |
| BioSample |
SAMN12722918 |
| SRA |
SRX6827300 |
