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| Status |
Public on May 09, 2017 |
| Title |
timepoint24 RNA-seq.fastq |
| Sample type |
SRA |
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| Source name |
Zea mays kernel_24 hpi
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| Organisms |
Zea mays; Aspergillus flavus |
| Characteristics |
maize development stage: Milk
maize cultivar: B73
aspergillus strain: NR3357
time point: 24 hrs post inoculation (hpi)
tissue: kernel
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| Treatment protocol |
A time course study was performed by pin bar inoculating one ear (per time point) of maize B73 with A. flavus NR3357 and harvesting at 0, 6, 12, 18, 24, 30, 36, 42, 48 and 72 hours post inoculation.
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| Growth protocol |
Maize B73 was grown in Clayton, NC during the years 2011 and 2013. Seeds were planted on April 16. Ears were hand pollinated from July 5-8 and covered with a paper bag.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Eight kernels per ear were ground and used for RNA isolation. Approximately one hundred milligrams of ground tissue was homogenized in a Virtis homogenizer (Virtis, Gardiner, NY) in Saturated Phenol, pH 6.6 for 2 min. Samples were then dissolved in Tris EDTA buffer, pH 8.0 (ACROS Organics, New Jersey, US), purified with 5:1 Acid Phenol: Chloroform, pH 4.5, and precipitated with ice-cold 100% ethanol overnight. Total RNA was purified again with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quality and concentration of RNA was analyzed using an RNA Pico chip on an Agilent Bioanalyzer (Agilent, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 11
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Default CLC mapping settings, trimming and fastqc quality control of the reads, for both Z. mays and A. flavus, were done with CLC workbench 4.9 (Qiagen, Hilden, Germany).
RPKM and count values were then generated from CLC.
Genome_build: (AGPv3, INSDC Assembly GCA_000005005.5, Apr 2013) and A. flavus (JCVI-afl1-v2.0, INSDC Assembly GCA_000006275.1, Jan 2009).
Supplementary_files_format_and_content: RPKM/Count values for each Sample.
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| Submission date |
Aug 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bryan Manyasi Musungu |
| E-mail(s) |
bryan.musungu@siu.edu
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| Organization name |
Southern Illinois University Carbondale
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| Department |
Plant Biology
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| Street address |
1125 Lincoln Dr.
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| City |
Carbondale |
| State/province |
IL |
| ZIP/Postal code |
62901 |
| Country |
USA |
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| Platform ID |
GPL22349 |
| Series (1) |
| GSE85860 |
A Network Approach of Gene Co-Expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways |
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| Relations |
| BioSample |
SAMN05597285 |
| SRA |
SRX2035808 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2285729_timepoint24_RNA-Seq.xlsx |
16.1 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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