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| Status |
Public on Jun 14, 2020 |
| Title |
4-4d_S12_L002_R1_001 |
| Sample type |
SRA |
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| Source name |
Kernel
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| Organisms |
Zea mays; Aspergillus flavus |
| Characteristics |
strain: B73/NR3357
tissue: Kernel
age: Milk stage
treatment: innoculated with Aspergillus flavus
timepoint: 4d
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| Treatment protocol |
A. flavus NRRL 3357, was grown on potato dextrose agar (PDA) and collected from plates by 0.05% (v/v) Triton X-100. The 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, 72, 96,120 and 144 hours post inoculation.
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| Growth protocol |
B73 was hand planted in Clayton NC. At about 20 days after pollination, husks were pulled back and kernels were pin bar inoculated with 3357. Husks were placed back over the ear, secured with a rubber band, bagged and the bag was stapled around the stalk. Kernels were harvested over time at 0h, 4h, 6h, 12h, 18h, 24h, 30h, 36h, 42h, 48h, 3d, 4d, 5d and 6d. Each time course was harvested from a single plot. There were 8 plots (8 reps).
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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 (Virtis) in Saturated Phenol, pH 6.6 (Fisher) for 2 min. Samples were then dissolved in Tris EDTA buffer, pH 8.0 (ACROS Organics), purified with 5:1 Acid Phenol: Chloroform, pH 4.5 (Fisher), and precipitated with ice-cold 100% ethanol (ACROS Organics) overnight. Total RNA was purified again with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The quality and concentration of RNA was analyzed using an RNA Pico chip on an Agilent Bioanalyzer.
libraries for sequencing utilizing the NEBNext Ultra Directional RNA Library Prep Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were trimmed with CLC Genomics Work Bench
Reads were mapped with CLC Genomics Work bench
Unique read counts and RPKM were extracted from the abundance measurements
Genome_build: B73 RefGen_V3 5b+ and Aspergillus_flavus.JCVI-afl1-v2.0.35
Supplementary_files_format_and_content: RPKM and read counts
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| Submission date |
Jul 26, 2017 |
| Last update date |
Jun 14, 2020 |
| Contact name |
Bryan Manyasi Musungu |
| E-mail(s) |
[email protected]
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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 |
GPL23833 |
| Series (1) |
| GSE101899 |
Use of Dual RNA-seq for Systems Biology Analysis of Zea mays and Aspergillus flavus plant microbe interaction |
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| Relations |
| BioSample |
SAMN07417047 |
| SRA |
SRX3038725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2718204_4-4d_S12_L002_R1_001_trimmed_RNA-Seq.csv.gz |
892.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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