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Sample GSM1613465

Query DataSets for GSM1613465

Status

Public on Feb 19, 2015

Title

WT3

Sample type

SRA

Source name

6dpi infected maize kernel

Organism

Fusarium verticillioides

Characteristics

strain: wild type

Growth protocol

Kernels of maize inbred B73 were submerged in deionized water and autoclaved for 15 min. Afterwards, the kernels were crushed slightly to disrupt the pericarp, and approximately 7 g of kernels (10-12 kernels) were placed in glass vials (20 ml) and autoclaved for 30 min. Four replicate vials of the WT and ∆fst1 were inoculated with 100 µl of 10^6 conidia/ml. Vials were incubated at 28°C for 6 days, then flash frozen in liquid nitrogen and stored at -80°C.

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from the content of each vial and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). Further purification was achieved by treatment with the DNA-Free RNA kit (Zymo Research, Irvine, CA, USA).
The Purdue Genetic Core Facility conducted quality assessment, processing, and sequencing of the RNA. The RNA samples had a RIN (RNA Integrity Number) over 7.0 as determined with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Paired-end sequences were obtained with an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA, USA). Sequence data were trimmed of adapters and filtered to remove low quality sequence and reads less than 30 nt.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

RNA sequence data from each sample were mapped to the reference genome of Gibberella moniliformis, which was downloaded (June 2014) from the Broad Institute Fusarium Comparative Database (http://www.broadinstitute.org).
Sequence data were mapped to the reference genome was done with CLC Genomics Workbench (version 7.0.4, CLC Bio, Boston), and gene expression was quantified as reads per kilobase per million mapped reads (RPKM)
Statistical analysis (pairwise t-testing) was also conducted with the CLC Genomics software
Genome_build: Gibberella moniliformis
Supplementary_files_format_and_content: Excel files include RPKM values for each sample and mean value for each strain

Submission date

Feb 18, 2015

Last update date

May 15, 2019

Contact name

Charles Peter Woloshuk

E-mail(s)

woloshuk@purdue.edu

Phone

765-494-3450

Organization name

Purdue University